MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000359125
Querying Taster for transcript #2: ENST00000627221
Querying Taster for transcript #3: ENST00000706989
Querying Taster for transcript #4: ENST00000625514
Querying Taster for transcript #5: ENST00000637193
Querying Taster for transcript #6: ENST00000360480
Querying Taster for transcript #7: ENST00000344462
Querying Taster for transcript #8: ENST00000629318
Querying Taster for transcript #9: ENST00000344425
Querying Taster for transcript #10: ENST00000713606
Querying Taster for transcript #11: ENST00000626839
Querying Taster for transcript #12: ENST00000629241
Querying Taster for transcript #13: ENST00000629676
Querying Taster for transcript #14: ENST00000370224
Querying Taster for transcript #15: ENST00000713605
Querying Taster for transcript #16: ENST00000713658
Querying Taster for transcript #17: ENST00000629498
MT speed 0.48 s - this script 2.967027 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000629498	KCNQ2	Deleterious	61\|39	3utr	No	Single base exchange	N/A
ENST00000713606	KCNQ2	Deleterious	84\|16	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000626839	KCNQ2	Deleterious	110\|90	without_aae	No	Single base exchange	Normal
ENST00000629676	KCNQ2	Deleterious	137\|63	without_aae	No	Single base exchange	Normal
ENST00000713658	KCNQ2	Benign	47\|53	3utr	No	Single base exchange	N/A
ENST00000627221	KCNQ2	Benign	62\|138	without_aae	No	Single base exchange	Normal
ENST00000629318	KCNQ2	Benign	66\|134	without_aae	No	Single base exchange	Normal
ENST00000706989	KCNQ2	Benign	69\|131	without_aae	No	Single base exchange	Normal
ENST00000713605	KCNQ2	Benign	69\|131	without_aae	No	Single base exchange	Normal
ENST00000344462	KCNQ2	Benign	80\|120	without_aae	No	Single base exchange	Normal
ENST00000359125(MANE Select)	KCNQ2	Benign	82\|118	without_aae	No	Single base exchange	Normal
ENST00000625514	KCNQ2	Benign	82\|118	without_aae	No	Single base exchange	Normal
ENST00000629241	KCNQ2	Benign	84\|116	without_aae	No	Single base exchange	Normal
ENST00000370224	KCNQ2	Benign	84\|116	without_aae	No	Single base exchange	Normal
ENST00000360480	KCNQ2	Benign	89\|111	without_aae	No	Single base exchange	Normal
ENST00000637193	KCNQ2	Benign	95\|105	without_aae	No	Single base exchange	Normal
ENST00000344425	KCNQ2	Benign	98\|102	without_aae	No	Single base exchange	Normal

MutationT@ster 2025

Variant:

20:63433874G>A_17_ENST00000629498

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: 3utr
Tree vote: 61|39 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.76, LOF (oe): 0.39, misssense (oe): 0.36, synonymous (oe): 0.92 ? (gnomAD)

Ensembl transcript ID

ENST00000629498.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1297C>T
g.38804C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLPRVASGRP ACPQGCEQAL RVTRACGPTD
HADHHWLRGQ VPPDLERQAP CGNLHPHRCL LLRAACSSGA AQAEAL*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1267

Theoretical NMD boundary in CDS

1024

Length of CDS

1041

Coding sequence (CDS) position

N/A

cDNA position

1297

gDNA position

38804

Chromosomal position

63433874

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_10_ENST00000713606

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 84|16 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

no data

Ensembl transcript ID

ENST00000713606.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1276C>T
g.38804C>T

AA changes

AAE:	L426F	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		426	P	V	G	L	E	I	L	R	H	Q	P	L	A	H	R	P	A	L	H	V	A	V	L	R
mutated	not conserved	426							L	R	H	Q	P	F	A	H	R	P	A	L	H	V	A	V	L
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QHRKTKQRHR ERKSSQARFS
LTYRLMPRAG LSPRPGRLEA EVPGPTHTPS ASGCPGPNQE VRKVTPRTGD TRQGPVGLEI
LRHQPLAHRP ALHVAVLRAN GHRAHVQVPP PGTCHQATVS FFIFHLFLNP TFCCSLF*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QHRKTKQRHR ERKSSQARFS
LTYRLMPRAG LSPRPGRLEA EVPGPTHTPS ASGCPGPNQE VRKVTPRTGD TRQGPVGLEI
LRHQPFAHRP ALHVAVLRAN GHRAHVQVPP PGTCHQATVS FFIFHLFLNP TFCCSLF*

Position of stopcodon in wt / mu CDS

1434 / 1434

Position (AA) of stopcodon in wt / mu AA sequence

478 / 478

Position of stopcodon in wt / mu cDNA

1626 / 1626

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1438

Theoretical NMD boundary in CDS

1195

Length of CDS

1434

Coding sequence (CDS) position

1276

cDNA position

1468

gDNA position

38804

Chromosomal position

63433874

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_11_ENST00000626839

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 110|90 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.28, LOF (oe): 0.17, misssense (oe): 0.69, synonymous (oe): 1.18 ? (gnomAD)

Ensembl transcript ID

ENST00000626839.2

Genbank transcript ID

NM_172106 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS
LKDRVFSSPR GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI
KGAASRQNSE EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES
LRPYDVMDVI EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS
MMGRLGKVEK QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE
HVDRHGCIVK IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS
LVRIPPPPAH ERSLSAYGGG NRASMEFLRQ EDTPGCRPPE GNLRDSDTSI SIPSVDHEEL
ERSFSGFSIS QSKENLDALN SCYAAVAPCA KVRPYIAEGE SDTDSDLCTP CGPPPRSATG
EGPFGDVGWA GPRK*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS
LKDRVFSSPR GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI
KGAASRQNSE EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES
LRPYDVMDVI EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS
MMGRLGKVEK QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE
HVDRHGCIVK IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS
LVRIPPPPAH ERSLSAYGGG NRASMEFLRQ EDTPGCRPPE GNLRDSDTSI SIPSVDHEEL
ERSFSGFSIS QSKENLDALN SCYAAVAPCA KVRPYIAEGE SDTDSDLCTP CGPPPRSATG
EGPFGDVGWA GPRK*

Position of stopcodon in wt / mu CDS

2565 / 2565

Position (AA) of stopcodon in wt / mu AA sequence

855 / 855

Position of stopcodon in wt / mu cDNA

2779 / 2779

Position of start ATG in wt / mu cDNA

215 / 215

Last intron/exon boundary

2047

Theoretical NMD boundary in CDS

1782

Length of CDS

2565

Coding sequence (CDS) position

1053

cDNA position

1267

gDNA position

38804

Chromosomal position

63433874

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_13_ENST00000629676

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Model: without_aae
Tree vote: 137|63 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.29, LOF (oe): 0.17, misssense (oe): 0.52, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000629676.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR DGLQRHAQGR RGLTEGSRTE APRAGGPAGR HPSARDPHGP
RVPAMPAPHA IAVCHPLAVT VAAASPFAPL PLAVCTFVHA PKNIS*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR DGLQRHAQGR RGLTEGSRTE APRAGGPAGR HPSARDPHGP
RVPAMPAPHA IAVCHPLAVT VAAASPFAPL PLAVCTFVHA PKNIS*

Position of stopcodon in wt / mu CDS

1938 / 1938

Position (AA) of stopcodon in wt / mu AA sequence

646 / 646

Position of stopcodon in wt / mu cDNA

2030 / 2030

Position of start ATG in wt / mu cDNA

93 / 93

Last intron/exon boundary

1771

Theoretical NMD boundary in CDS

1628

Length of CDS

1938

Coding sequence (CDS) position

1053

cDNA position

1145

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_16_ENST00000713658

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: 3utr
Tree vote: 47|53 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

no data

Ensembl transcript ID

ENST00000713658.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

3'UTR

DNA changes

cDNA.1327C>T
g.38804C>T

AA changes

N/A

Frameshift

No

Length of protein

N/A

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

N/A

poly(A) signal

polyA signal ok

AA sequence altered

N/A

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLPRVASGRP ACPQGCEQAL RVTRACGPTD
HADHHWLRGQ VPPDLERQAP CGNLHPHRCL LLRAACRHLG VWVCPEGSGA AQAEAL*

Mutated AA sequence

Position of stopcodon in wt / mu CDS

N/A

Position (AA) of stopcodon in wt / mu AA sequence

N/A

Position of stopcodon in wt / mu cDNA

N/A

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1297

Theoretical NMD boundary in CDS

1054

Length of CDS

1071

Coding sequence (CDS) position

N/A

cDNA position

1327

gDNA position

38804

Chromosomal position

63433874

Speed

0.11 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:63433874G>A_2_ENST00000627221

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 62|138 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.39, LOF (oe): 0.18, misssense (oe): 0.59, synonymous (oe): 1.09 ? (gnomAD)

Ensembl transcript ID

ENST00000627221.3

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
ASLPGEDIVD DKSCPCEFVT EDLTPGLKVS IRAVCVMRFL VSKRKFKESL RPYDVMDVIE
QYSAGHLDML SRIKSLQSRV DQIVGRGPAI TDKDRTKGPA EAELPEDPSM MGRLGKVEKQ
VLSMEKKLDF LVNIYMQRMG IPPTETEAYF GAKEPEPAPP YHSPEDSREH VDRHGCIVKI
VRSSSSTGQK NFSAPPAAPP VQCPPSTSWQ PQSHPRQGHG TSPVGDHGSL VRIPPPPAHE
RSLSAYGGGN RASMEFLRQE DTPGCRPPEG NLRDSDTSIS IPSVDHEELE RSFSGFSISQ
SKENLDALNS CYAAVAPCAK VRPYIAEGES DTDSDLCTPC GPPPRSATGE GPFGDVGWAG
PRK*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
ASLPGEDIVD DKSCPCEFVT EDLTPGLKVS IRAVCVMRFL VSKRKFKESL RPYDVMDVIE
QYSAGHLDML SRIKSLQSRV DQIVGRGPAI TDKDRTKGPA EAELPEDPSM MGRLGKVEKQ
VLSMEKKLDF LVNIYMQRMG IPPTETEAYF GAKEPEPAPP YHSPEDSREH VDRHGCIVKI
VRSSSSTGQK NFSAPPAAPP VQCPPSTSWQ PQSHPRQGHG TSPVGDHGSL VRIPPPPAHE
RSLSAYGGGN RASMEFLRQE DTPGCRPPEG NLRDSDTSIS IPSVDHEELE RSFSGFSISQ
SKENLDALNS CYAAVAPCAK VRPYIAEGES DTDSDLCTPC GPPPRSATGE GPFGDVGWAG
PRK*

Position of stopcodon in wt / mu CDS

2532 / 2532

Position (AA) of stopcodon in wt / mu AA sequence

844 / 844

Position of stopcodon in wt / mu cDNA

2724 / 2724

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1992

Theoretical NMD boundary in CDS

1749

Length of CDS

2532

Coding sequence (CDS) position

1053

cDNA position

1245

gDNA position

38804

Chromosomal position

63433874

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_8_ENST00000629318

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 66|134 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.32, LOF (oe): 0.00, misssense (oe): 0.58, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000629318.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.534C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVLIASIAVL AAGSQGNVFA TSALRSLRFL QILRMIRMDR RGGTWKLLGS VVYAHSKELV
TAWYIGFLCL ILASFLVYLA EKGENDHFDT YADALWWGLI TLTTIGYGDK YPQTWNGRLL
AATFTLIGVS FFALPAGILG SGFALKVQEQ HRQKHFEKRR NPAAGLIQSA WRFYATNLSR
TDLHSTWQYY ERTVTVPMYR LIPPLNQLEL LRNLKSKSGL AFRKDPPPEP SPSQKVSLKD
RVFSSPRGVA AKGKGSPQAQ TVRRSPSADQ SLEDSPSKVP KSWSFGDRSR ARQAFRIKGA
ASRQNSEEAS LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP
YDVMDVIEQY SAGHLDMLSR IKSLQSRQEP RLPVQQGTRT GWASGTKPTV AHGGSAGGVW
AGPPPHPRRP LSASVVSSQS LF*

Mutated AA sequence

MVLIASIAVL AAGSQGNVFA TSALRSLRFL QILRMIRMDR RGGTWKLLGS VVYAHSKELV
TAWYIGFLCL ILASFLVYLA EKGENDHFDT YADALWWGLI TLTTIGYGDK YPQTWNGRLL
AATFTLIGVS FFALPAGILG SGFALKVQEQ HRQKHFEKRR NPAAGLIQSA WRFYATNLSR
TDLHSTWQYY ERTVTVPMYR LIPPLNQLEL LRNLKSKSGL AFRKDPPPEP SPSQKVSLKD
RVFSSPRGVA AKGKGSPQAQ TVRRSPSADQ SLEDSPSKVP KSWSFGDRSR ARQAFRIKGA
ASRQNSEEAS LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP
YDVMDVIEQY SAGHLDMLSR IKSLQSRQEP RLPVQQGTRT GWASGTKPTV AHGGSAGGVW
AGPPPHPRRP LSASVVSSQS LF*

Position of stopcodon in wt / mu CDS

1329 / 1329

Position (AA) of stopcodon in wt / mu AA sequence

443 / 443

Position of stopcodon in wt / mu cDNA

1660 / 1660

Position of start ATG in wt / mu cDNA

332 / 332

Last intron/exon boundary

1359

Theoretical NMD boundary in CDS

977

Length of CDS

1329

Coding sequence (CDS) position

534

cDNA position

865

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_3_ENST00000706989

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 69|131 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

no data

Ensembl transcript ID

ENST00000706989.1

Genbank transcript ID

NM_001382235 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS
LKDRVFSSPR GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI
KGAASRQNSE EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES
LRPYDVMDVI EQYSAGHLDM LSRIKSLQSR IDMIVGPPPP STPRHKKYPT KGPTAPPRES
PQYSPRVDQI VGRGPAITDK DRTKGPAEAE LPEDPSMMGR LGKVEKQVLS MEKKLDFLVN
IYMQRMGIPP TETEAYFGAK EPEPAPPYHS PEDSREHVDR HGCIVKIVRS SSSTGQKNFS
APPAAPPVQC PPSTSWQPQS HPRQGHGTSP VGDHGSLVRI PPPPAHERSL SAYGGGNRAS
MEFLRQEDTP GCRPPEGNLR DSDTSISIPS VDHEELERSF SGFSISQSKE NLDALNSCYA
AVAPCAKVRP YIAEGESDTD SDLCTPCGPP PRSATGEGPF GDVGWAGPRK *

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS
LKDRVFSSPR GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI
KGAASRQNSE EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES
LRPYDVMDVI EQYSAGHLDM LSRIKSLQSR IDMIVGPPPP STPRHKKYPT KGPTAPPRES
PQYSPRVDQI VGRGPAITDK DRTKGPAEAE LPEDPSMMGR LGKVEKQVLS MEKKLDFLVN
IYMQRMGIPP TETEAYFGAK EPEPAPPYHS PEDSREHVDR HGCIVKIVRS SSSTGQKNFS
APPAAPPVQC PPSTSWQPQS HPRQGHGTSP VGDHGSLVRI PPPPAHERSL SAYGGGNRAS
MEFLRQEDTP GCRPPEGNLR DSDTSISIPS VDHEELERSF SGFSISQSKE NLDALNSCYA
AVAPCAKVRP YIAEGESDTD SDLCTPCGPP PRSATGEGPF GDVGWAGPRK *

Position of stopcodon in wt / mu CDS

2673 / 2673

Position (AA) of stopcodon in wt / mu AA sequence

891 / 891

Position of stopcodon in wt / mu cDNA

2865 / 2865

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

2133

Theoretical NMD boundary in CDS

1890

Length of CDS

2673

Coding sequence (CDS) position

1053

cDNA position

1245

gDNA position

38804

Chromosomal position

63433874

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_15_ENST00000713605

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 69|131 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

no data

Ensembl transcript ID

ENST00000713605.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV AAKGKGSPQA
QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD
KSCPCEFVTE DLTPGLKVSI RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS
RIKSLQSRVD QIVGRGPAIT DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL
VNIYMQRMGI PPTETEAYFG AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN
FSAPPAAPPV QCPPSTSWQP QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR
ASMEFLRQED TPGCRPPEGN LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC
YAAVAPCAKV RPYIAEGESD TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV AAKGKGSPQA
QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD
KSCPCEFVTE DLTPGLKVSI RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS
RIKSLQSRVD QIVGRGPAIT DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL
VNIYMQRMGI PPTETEAYFG AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN
FSAPPAAPPV QCPPSTSWQP QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR
ASMEFLRQED TPGCRPPEGN LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC
YAAVAPCAKV RPYIAEGESD TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*

Position of stopcodon in wt / mu CDS

2499 / 2499

Position (AA) of stopcodon in wt / mu AA sequence

833 / 833

Position of stopcodon in wt / mu cDNA

2691 / 2691

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1959

Theoretical NMD boundary in CDS

1716

Length of CDS

2499

Coding sequence (CDS) position

1053

cDNA position

1245

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_7_ENST00000344462

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 80|120 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.31, LOF (oe): 0.20, misssense (oe): 0.69, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000344462.8

Genbank transcript ID

NM_172108 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV
AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEAS
LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP YDVMDVIEQY
SAGHLDMLSR IKSLQSRVDQ IVGRGPAITD KDRTKGPAEA ELPEDPSMMG RLGKVEKQVL
SMEKKLDFLV NIYMQRMGIP PTETEAYFGA KEPEPAPPYH SPEDSREHVD RHGCIVKIVR
SSSSTGQKNF SAPPAAPPVQ CPPSTSWQPQ SHPRQGHGTS PVGDHGSLVR IPPPPAHERS
LSAYGGGNRA SMEFLRQEDT PGCRPPEGNL RDSDTSISIP SVDHEELERS FSGFSISQSK
ENLDALNSCY AAVAPCAKVR PYIAEGESDT DSDLCTPCGP PPRSATGEGP FGDVGWAGPR
K*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV
AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEAS
LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP YDVMDVIEQY
SAGHLDMLSR IKSLQSRVDQ IVGRGPAITD KDRTKGPAEA ELPEDPSMMG RLGKVEKQVL
SMEKKLDFLV NIYMQRMGIP PTETEAYFGA KEPEPAPPYH SPEDSREHVD RHGCIVKIVR
SSSSTGQKNF SAPPAAPPVQ CPPSTSWQPQ SHPRQGHGTS PVGDHGSLVR IPPPPAHERS
LSAYGGGNRA SMEFLRQEDT PGCRPPEGNL RDSDTSISIP SVDHEELERS FSGFSISQSK
ENLDALNSCY AAVAPCAKVR PYIAEGESDT DSDLCTPCGP PPRSATGEGP FGDVGWAGPR
K*

Position of stopcodon in wt / mu CDS

2526 / 2526

Position (AA) of stopcodon in wt / mu AA sequence

842 / 842

Position of stopcodon in wt / mu cDNA

2572 / 2572

Position of start ATG in wt / mu cDNA

47 / 47

Last intron/exon boundary

1840

Theoretical NMD boundary in CDS

1743

Length of CDS

2526

Coding sequence (CDS) position

1053

cDNA position

1099

gDNA position

38804

Chromosomal position

63433874

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_1_ENST00000359125

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 82|118 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.29, LOF (oe): 0.19, misssense (oe): 0.70, synonymous (oe): 1.18 ? (gnomAD)

Ensembl transcript ID

ENST00000359125.7

Genbank transcript ID

NM_172107 (exact from MANE)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSKGSP
CRGPLCGCCP GRSSQKVSLK DRVFSSPRGV AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV
PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD KSCPCEFVTE DLTPGLKVSI
RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS RIKSLQSRVD QIVGRGPAIT
DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL VNIYMQRMGI PPTETEAYFG
AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN FSAPPAAPPV QCPPSTSWQP
QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR ASMEFLRQED TPGCRPPEGN
LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC YAAVAPCAKV RPYIAEGESD
TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYSSQTQTYG ASRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSKGSP
CRGPLCGCCP GRSSQKVSLK DRVFSSPRGV AAKGKGSPQA QTVRRSPSAD QSLEDSPSKV
PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD KSCPCEFVTE DLTPGLKVSI
RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS RIKSLQSRVD QIVGRGPAIT
DKDRTKGPAE AELPEDPSMM GRLGKVEKQV LSMEKKLDFL VNIYMQRMGI PPTETEAYFG
AKEPEPAPPY HSPEDSREHV DRHGCIVKIV RSSSSTGQKN FSAPPAAPPV QCPPSTSWQP
QSHPRQGHGT SPVGDHGSLV RIPPPPAHER SLSAYGGGNR ASMEFLRQED TPGCRPPEGN
LRDSDTSISI PSVDHEELER SFSGFSISQS KENLDALNSC YAAVAPCAKV RPYIAEGESD
TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK*

Position of stopcodon in wt / mu CDS

2619 / 2619

Position (AA) of stopcodon in wt / mu AA sequence

873 / 873

Position of stopcodon in wt / mu cDNA

2811 / 2811

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

2079

Theoretical NMD boundary in CDS

1836

Length of CDS

2619

Coding sequence (CDS) position

1053

cDNA position

1245

gDNA position

38804

Chromosomal position

63433874

Speed

0.03 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_4_ENST00000625514

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 82|118 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.33, LOF (oe): 0.21, misssense (oe): 0.62, synonymous (oe): 1.20 ? (gnomAD)

Ensembl transcript ID

ENST00000625514.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV AAKGKGSPQA
QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD
KSCPCEFVTE DLTPGLKVSI RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS
RIKSLQSRID MIVGPPPPST PRHKKYPTKG PTAPPRESPQ YSPRVDQIVG RGPAITDKDR
TKGPAEAELP EDPSMMGRLG KVEKQVLSME KKLDFLVNIY MQRMGIPPTE TEAYFGAKEP
EPAPPYHSPE DSREHVDRHG CIVKIVRSSS STGQKNFSAP PAAPPVQCPP STSWQPQSHP
RQGHGTSPVG DHGSLGRAPE TRAGQEGSHG GVSH*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSPRGV AAKGKGSPQA
QTVRRSPSAD QSLEDSPSKV PKSWSFGDRS RARQAFRIKG AASRQNSEEA SLPGEDIVDD
KSCPCEFVTE DLTPGLKVSI RAVCVMRFLV SKRKFKESLR PYDVMDVIEQ YSAGHLDMLS
RIKSLQSRID MIVGPPPPST PRHKKYPTKG PTAPPRESPQ YSPRVDQIVG RGPAITDKDR
TKGPAEAELP EDPSMMGRLG KVEKQVLSME KKLDFLVNIY MQRMGIPPTE TEAYFGAKEP
EPAPPYHSPE DSREHVDRHG CIVKIVRSSS STGQKNFSAP PAAPPVQCPP STSWQPQSHP
RQGHGTSPVG DHGSLGRAPE TRAGQEGSHG GVSH*

Position of stopcodon in wt / mu CDS

2265 / 2265

Position (AA) of stopcodon in wt / mu AA sequence

755 / 755

Position of stopcodon in wt / mu cDNA

2357 / 2357

Position of start ATG in wt / mu cDNA

93 / 93

Last intron/exon boundary

2297

Theoretical NMD boundary in CDS

2154

Length of CDS

2265

Coding sequence (CDS) position

1053

cDNA position

1145

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_12_ENST00000629241

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 84|116 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.33, LOF (oe): 0.21, misssense (oe): 0.62, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000629241.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS MMGRLGKVEK
QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE HVDRHGCIVK
IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS LGRAPETRAG
QEGSHGGVSH *

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS MMGRLGKVEK
QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE HVDRHGCIVK
IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS LGRAPETRAG
QEGSHGGVSH *

Position of stopcodon in wt / mu CDS

2193 / 2193

Position (AA) of stopcodon in wt / mu AA sequence

731 / 731

Position of stopcodon in wt / mu cDNA

2285 / 2285

Position of start ATG in wt / mu cDNA

93 / 93

Last intron/exon boundary

2225

Theoretical NMD boundary in CDS

2082

Length of CDS

2193

Coding sequence (CDS) position

1053

cDNA position

1145

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

20:63433874G>A_14_ENST00000370224

Back to summary table

Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 84|116 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.33, LOF (oe): 0.21, misssense (oe): 0.62, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000370224.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR IDMIVGPPPP STPRHKKYPT KGPTAPPRES PQYSPRVDQI
VGRGPAITDK DRTKGPAEAE LPEDPSMMGR LGKVEKQVLS MEKKLDFLVN IYMQRMGIPP
TETEAYFGAK EPEPAPPYHS PEDSREHVDR HGCIVKIVRS SSSTGQKNFS APPAAPPVQC
PPSTSWQPQS HPRQGHGTSP VGDHGSLGRA PETRAGQEGS HGGVSH*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR IDMIVGPPPP STPRHKKYPT KGPTAPPRES PQYSPRVDQI
VGRGPAITDK DRTKGPAEAE LPEDPSMMGR LGKVEKQVLS MEKKLDFLVN IYMQRMGIPP
TETEAYFGAK EPEPAPPYHS PEDSREHVDR HGCIVKIVRS SSSTGQKNFS APPAAPPVQC
PPSTSWQPQS HPRQGHGTSP VGDHGSLGRA PETRAGQEGS HGGVSH*

Position of stopcodon in wt / mu CDS

2301 / 2301

Position (AA) of stopcodon in wt / mu AA sequence

767 / 767

Position of stopcodon in wt / mu cDNA

2436 / 2436

Position of start ATG in wt / mu cDNA

136 / 136

Last intron/exon boundary

2376

Theoretical NMD boundary in CDS

2190

Length of CDS

2301

Coding sequence (CDS) position

1053

cDNA position

1188

gDNA position

38804

Chromosomal position

63433874

Speed

0.02 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:63433874G>A_6_ENST00000360480

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 89|111 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.29, LOF (oe): 0.18, misssense (oe): 0.68, synonymous (oe): 1.19 ? (gnomAD)

Ensembl transcript ID

ENST00000360480.7

Genbank transcript ID

NM_004518 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS MMGRLGKVEK
QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE HVDRHGCIVK
IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS LVRIPPPPAH
ERSLSAYGGG NRASMEFLRQ EDTPGCRPPE GNLRDSDTSI SIPSVDHEEL ERSFSGFSIS
QSKENLDALN SCYAAVAPCA KVRPYIAEGE SDTDSDLCTP CGPPPRSATG EGPFGDVGWA
GPRK*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRLIPPLNQ LELLRNLKSK SGLAFRKDPP PEPSPSQKVS LKDRVFSSPR
GVAAKGKGSP QAQTVRRSPS ADQSLEDSPS KVPKSWSFGD RSRARQAFRI KGAASRQNSE
EASLPGEDIV DDKSCPCEFV TEDLTPGLKV SIRAVCVMRF LVSKRKFKES LRPYDVMDVI
EQYSAGHLDM LSRIKSLQSR VDQIVGRGPA ITDKDRTKGP AEAELPEDPS MMGRLGKVEK
QVLSMEKKLD FLVNIYMQRM GIPPTETEAY FGAKEPEPAP PYHSPEDSRE HVDRHGCIVK
IVRSSSSTGQ KNFSAPPAAP PVQCPPSTSW QPQSHPRQGH GTSPVGDHGS LVRIPPPPAH
ERSLSAYGGG NRASMEFLRQ EDTPGCRPPE GNLRDSDTSI SIPSVDHEEL ERSFSGFSIS
QSKENLDALN SCYAAVAPCA KVRPYIAEGE SDTDSDLCTP CGPPPRSATG EGPFGDVGWA
GPRK*

Position of stopcodon in wt / mu CDS

2535 / 2535

Position (AA) of stopcodon in wt / mu AA sequence

845 / 845

Position of stopcodon in wt / mu cDNA

2577 / 2577

Position of start ATG in wt / mu cDNA

43 / 43

Last intron/exon boundary

1845

Theoretical NMD boundary in CDS

1752

Length of CDS

2535

Coding sequence (CDS) position

1053

cDNA position

1095

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:63433874G>A_5_ENST00000637193

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 95|105 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.27, LOF (oe): 0.16, misssense (oe): 0.67, synonymous (oe): 1.16 ? (gnomAD)

Ensembl transcript ID

ENST00000637193.1

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.534C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVLIASIAVL AAGSQGNVFA TSALRSLRFL QILRMIRMDR RGGTWKLLGS VVYAHSKELV
TAWYIGFLCL ILASFLVYLA EKGENDHFDT YADALWWGLI TLTTIGYGDK YPQTWNGRLL
AATFTLIGVS FFALPAGILG SGFALKVQEQ HRQKHFEKRR NPAAGLIQSA WRFYATNLSR
TDLHSTWQYY ERTVTVPMYR LIPPLNQLEL LRNLKSKSGL AFRKDPPPEP SPSQKVSLKD
RVFSSPRGVA AKGKGSPQAQ TVRRSPSADQ SLEDSPSKVP KSWSFGDRSR ARQAFRIKGA
ASRQNSEEAS LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP
YDVMDVIEQY SAGHLDMLSR IKSLQSRVDQ IVGRGPAITD KDRTKGPAEA ELPEDPSMMG
RLGKVEKQVL SMEKKLDFLV NIYMQRMGIP PTETEAYFGA KEPEPAPPYH SPEDSREHVD
RHGCIVKIVR SSSSTGQKNF SAPPAAPPVQ CPPSTSWQPQ SHPRQGHGTS PVGDHGSLVR
IPPPPAHERS LSAYGGGNRA SMEFLRQEDT PGCRPPEGNL RDSDTSISIP SVDHEELERS
FSGFSISQSK ENLDALNSCY AAVAPCAKVR PYIAEGESDT DSDLCTPCGP PPRSATGEGP
FGDVGWAGPR K*

Mutated AA sequence

MVLIASIAVL AAGSQGNVFA TSALRSLRFL QILRMIRMDR RGGTWKLLGS VVYAHSKELV
TAWYIGFLCL ILASFLVYLA EKGENDHFDT YADALWWGLI TLTTIGYGDK YPQTWNGRLL
AATFTLIGVS FFALPAGILG SGFALKVQEQ HRQKHFEKRR NPAAGLIQSA WRFYATNLSR
TDLHSTWQYY ERTVTVPMYR LIPPLNQLEL LRNLKSKSGL AFRKDPPPEP SPSQKVSLKD
RVFSSPRGVA AKGKGSPQAQ TVRRSPSADQ SLEDSPSKVP KSWSFGDRSR ARQAFRIKGA
ASRQNSEEAS LPGEDIVDDK SCPCEFVTED LTPGLKVSIR AVCVMRFLVS KRKFKESLRP
YDVMDVIEQY SAGHLDMLSR IKSLQSRVDQ IVGRGPAITD KDRTKGPAEA ELPEDPSMMG
RLGKVEKQVL SMEKKLDFLV NIYMQRMGIP PTETEAYFGA KEPEPAPPYH SPEDSREHVD
RHGCIVKIVR SSSSTGQKNF SAPPAAPPVQ CPPSTSWQPQ SHPRQGHGTS PVGDHGSLVR
IPPPPAHERS LSAYGGGNRA SMEFLRQEDT PGCRPPEGNL RDSDTSISIP SVDHEELERS
FSGFSISQSK ENLDALNSCY AAVAPCAKVR PYIAEGESDT DSDLCTPCGP PPRSATGEGP
FGDVGWAGPR K*

Position of stopcodon in wt / mu CDS

2016 / 2016

Position (AA) of stopcodon in wt / mu AA sequence

672 / 672

Position of stopcodon in wt / mu cDNA

2418 / 2418

Position of start ATG in wt / mu cDNA

403 / 403

Last intron/exon boundary

1686

Theoretical NMD boundary in CDS

1233

Length of CDS

2016

Coding sequence (CDS) position

534

cDNA position

936

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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MutationT@ster 2025

Variant:

20:63433874G>A_9_ENST00000344425

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Prediction:

BenignPermalink

Summary:

Model: without_aae
Tree vote: 98|102 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr20:63433874G>A (GRCh38)

Gene symbol

KCNQ2

Gene constraints

LOEUF: 0.44, LOF (oe): 0.24, misssense (oe): 0.47, synonymous (oe): 1.24 ? (gnomAD)

Ensembl transcript ID

ENST00000344425.8

Genbank transcript ID

NM_172109 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1053C>T
g.38804C>T

AA changes

no AA changes

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'A' was not found in gnomAD

Protein conservation

N/A

Protein features

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.633	0.382
	-0.625	0.105
(flanking)	6.746	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

N/A

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

No

Chromosome

20

Strand

-1

Original gDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered gDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Original cDNA sequence snippet

AGATTCTACGCCACCAACCTCTCGCGCACAGACCTGCACTC

Altered cDNA sequence snippet

AGATTCTACGCCACCAACCTTTCGCGCACAGACCTGCACTC

Wildtype AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRYRRRAPA TKQLFHFLFS ICS*

Mutated AA sequence

MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG
GAGAGKPPKR NAFYRKLQNF LYNVLERPRG WAFIYHAYVF LLVFSCLVLS VFSTIKEYEK
SSEGALYILE IVTIVVFGVE YFVRIWAAGC CCRYRGWRGR LKFARKPFCV IDIMVLIASI
AVLAAGSQGN VFATSALRSL RFLQILRMIR MDRRGGTWKL LGSVVYAHSK ELVTAWYIGF
LCLILASFLV YLAEKGENDH FDTYADALWW GLITLTTIGY GDKYPQTWNG RLLAATFTLI
GVSFFALPAG ILGSGFALKV QEQHRQKHFE KRRNPAAGLI QSAWRFYATN LSRTDLHSTW
QYYERTVTVP MYRYRRRAPA TKQLFHFLFS ICS*

Position of stopcodon in wt / mu CDS

1182 / 1182

Position (AA) of stopcodon in wt / mu AA sequence

394 / 394

Position of stopcodon in wt / mu cDNA

1374 / 1374

Position of start ATG in wt / mu cDNA

193 / 193

Last intron/exon boundary

1215

Theoretical NMD boundary in CDS

972

Length of CDS

1182

Coding sequence (CDS) position

1053

cDNA position

1245

gDNA position

38804

Chromosomal position

63433874

Speed

0.01 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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