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: ENST00000378610
Querying Taster for transcript #2: ENST00000274695
MT speed 0.2 s - this script 2.624727 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000274695(MANE Select)	CDKAL1	Deleterious	95\|5	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000378610	CDKAL1	Deleterious	97\|3	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

6:20955443C>A_2_ENST00000274695

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:20955443C>A (GRCh38)

Gene symbol

CDKAL1

Gene constraints

LOEUF: 0.64, LOF (oe): 0.39, misssense (oe): 0.88, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000274695.8

Genbank transcript ID

NM_017774 (exact from MANE)

UniProt / AlphaMissense peptide

CDKAL_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.767C>A
g.420987C>A

AA changes

AAE:	T256N	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1347100951
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA	Alignment
Human		256	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I	G
mutated	not conserved	256	S	F	Q	E	G	V	C	E	I	W	L	N	S	E	D	T	G	A	Y	G	R	D	I
Ptroglodytes	all identical	256	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Mmulatta	all identical	256	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Fcatus	all identical	255	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Mmusculus	all identical	255	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Ggallus	all identical	254	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Trubripes	all identical	245	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Drerio	no homologue
Dmelanogaster	all identical	263	S	F	A	E	G	C	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I
Celegans	all identical	117										W	L	T	S	E	D	L	G	A	W	G	R	D	I
Xtropicalis	all identical	319	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I

Protein features

Start (aa)	End (aa)	Feature	Details
1	579	CHAIN		lost
200	431	DOMAIN	Radical SAM core	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.687	1
	7.35	1
(flanking)	5.564	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

25

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

6

Strand

1

Original gDNA sequence snippet

TGTTTGTGAGATATGGTTGACCAGTGAAGACACGGGGGCTT

Altered gDNA sequence snippet

TGTTTGTGAGATATGGTTGAACAGTGAAGACACGGGGGCTT

Original cDNA sequence snippet

TGTTTGTGAGATATGGTTGACCAGTGAAGACACGGGGGCTT

Altered cDNA sequence snippet

TGTTTGTGAGATATGGTTGAACAGTGAAGACACGGGGGCTT

Wildtype AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLTSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

Mutated AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLNSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

Position of stopcodon in wt / mu CDS

1740 / 1740

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

580 / 580

Position of stopcodon in wt / mu cDNA

1907 / 1907

Position of start ATG in wt / mu cDNA

168 / 168

Last intron/exon boundary

1715

Theoretical NMD boundary in CDS

1497

Length of CDS

1740

Coding sequence (CDS) position

767

cDNA position

934

gDNA position

420987

Chromosomal position

20955443

Speed

0.09 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:

6:20955443C>A_1_ENST00000378610

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:20955443C>A (GRCh38)

Gene symbol

CDKAL1

Gene constraints

LOEUF: 0.64, LOF (oe): 0.39, misssense (oe): 0.88, synonymous (oe): 0.97 ? (gnomAD)

Ensembl transcript ID

ENST00000378610.1

Genbank transcript ID

UniProt / AlphaMissense peptide

CDKAL_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.767C>A
g.420987C>A

AA changes

AAE:	T256N	?
Score:	65

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1347100951
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	0	8	8

Protein conservation

Species	Match	AA	Alignment
Human		256	S	F	Q	E	G	V	C	E	I	W	L	T	S	E	D	T	G	A	Y	G	R	D	I	G
mutated	not conserved	256	S	F	Q	E	G	V	C	E	I	W	L	N	S	E	D	T	G	A	Y	G	R	D	I
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

Start (aa)	End (aa)	Feature	Details
1	579	CHAIN		lost
200	431	DOMAIN	Radical SAM core	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	8.687	1
	7.35	1
(flanking)	5.564	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

25

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

6

Strand

1

Original gDNA sequence snippet

TGTTTGTGAGATATGGTTGACCAGTGAAGACACGGGGGCTT

Altered gDNA sequence snippet

TGTTTGTGAGATATGGTTGAACAGTGAAGACACGGGGGCTT

Original cDNA sequence snippet

TGTTTGTGAGATATGGTTGACCAGTGAAGACACGGGGGCTT

Altered cDNA sequence snippet

TGTTTGTGAGATATGGTTGAACAGTGAAGACACGGGGGCTT

Wildtype AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLTSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

Mutated AA sequence

MPSASCDTLL DDIEDIVSQE DSKPQDRHFV RKDVVPKVRR RNTQKYLQEE ENSPPSDSTI
PGIQKIWIRT WGCSHNNSDG EYMAGQLAAY GYKITENASD ADLWLLNSCT VKNPAEDHFR
NSIKKAQEEN KKIVLAGCVP QAQPRQDYLK GLSIIGVQQI DRVVEVVEET IKGHSVRLLG
QKKDNGRRLG GARLDLPKIR KNPLIEIISI NTGCLNACTY CKTKHARGNL ASYPIDELVD
RAKQSFQEGV CEIWLNSEDT GAYGRDIGTN LPTLLWKLVE VIPEGAMLRL GMTNPPYILE
HLEEMAKILN HPRVYAFLHI PVQSASDSVL MEMKREYCVA DFKRVVDFLK EKVPGITIAT
DIICGFPGET DQDFQETVKL VEEYKFPSLF INQFYPRPGT PAAKMEQVPA QVKKQRTKDL
SRVFHSYSPY DHKIGERQQV LVTEESFDSK FYVAHNQFYE QVLVPKNPAF MGKMVEVDIY
ESGKHFMKGQ PVSDAKVYTP SISKPLAKGE VSGLTKDFRN GLGNQLSSGS HTSAASQCDS
ASSRMVLPMP RLHQDCALRM SVGLALLGLL FAFFVKVYN*

Position of stopcodon in wt / mu CDS

1740 / 1740

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

580 / 580

Position of stopcodon in wt / mu cDNA

1750 / 1750

Position of start ATG in wt / mu cDNA

11 / 11

Last intron/exon boundary

1558

Theoretical NMD boundary in CDS

1497

Length of CDS

1740

Coding sequence (CDS) position

767

cDNA position

777

gDNA position

420987

Chromosomal position

20955443

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