MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000607772
Querying Taster for transcript #2: ENST00000673182
Querying Taster for transcript #3: ENST00000479339
MT speed 0.86 s - this script 3.244029 s

Transcript summary:

Permalink

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
ENST00000607772(MANE Select)	CNKSR3	Deleterious	96\|4	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000479339	CNKSR3	Deleterious	96\|4	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

6:154406465G>T_1_ENST00000607772

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:154406465G>T (GRCh38)

Gene symbol

CNKSR3

Gene constraints

LOEUF: 0.67, LOF (oe): 0.48, misssense (oe): 0.91, synonymous (oe): 0.96 ? (gnomAD)

Ensembl transcript ID

ENST00000607772.6

Genbank transcript ID

NM_173515 (exact from MANE), NM_001368117 (by similarity), NM_001368116 (by similarity)

UniProt / AlphaMissense peptide

CNKR3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1557C>A
g.104221C>A

AA changes

AAE:	F519L	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs146307807
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	59	59

Protein conservation

Species	Match	AA	Alignment
Human		519	N	S	D	L	H	S	S	A	T	I	P	F	Q	E	E	G	T	K	K	K	S	G	S	S
mutated	not conserved	519	N	S	D	L	H	S	S	A	T	I	P	L	Q	E	E	G	T	K	K	K	S	G	S
Ptroglodytes	all identical	519	N	S	D	L	H	S	S	A	T	I	P	F	Q	E	E	G	T	K	K	K	S	G	S
Mmulatta	all identical	519	N	S	D	L	H	S	S	A	T	I	P	F	Q	E	E	G	T	K	K	K	S	G	S
Fcatus	no alignment	n/a
Mmusculus	all identical	519	N	S	D	L	H	S	S	A	T	I	P	F	Q	E	E	G	S	K	K	K	S	A	S
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	555	CHAIN		lost
325	546	DOMAIN	DUF1170	lost
517	537	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	7.642	1
	2.263	1
(flanking)	5.25	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

6

Strand

-1

Original gDNA sequence snippet

AGCAGCGCCACGATTCCATTCCAGGAGGAAGGGACCAAAAA

Altered gDNA sequence snippet

AGCAGCGCCACGATTCCATTACAGGAGGAAGGGACCAAAAA

Original cDNA sequence snippet

AGCAGCGCCACGATTCCATTCCAGGAGGAAGGGACCAAAAA

Altered cDNA sequence snippet

AGCAGCGCCACGATTCCATTACAGGAGGAAGGGACCAAAAA

Wildtype AA sequence

MEPVTKWSPK QVVDWTRGLD DCLQQYVHKF EREKINGEQL LQISHQDLEE LGVTRIGHQE
LVLEAVDLLC ALNYGLETDN MKNLVLKLRA SSHNLQNYIS SRRKSPAYDG NTSRKAPNEF
LTSVVELIGA AKALLAWLDR APFTGITDFS VTKNKIIQLC LDLTTTVQKD CFVAEMEDKV
LTVVKVLNGI CDKTIRSTTD PVMSQCACLE EVHLPNIKPG EGLGMYIKST YDGLHVITGT
TENSPADRSQ KIHAGDEVIQ VNQQTVVGWQ LKNLVKKLRE NPTGVVLLLK KRPTGSFNFT
PAPLKNLRWK PPLVQTSPPP ATTQSPESTM DTSLKKEKSA ILDLYIPPPP AVPYSPRDEN
GSFVYGGSSK CKQPLPGPKG SESPNSFLDQ ESRRRRFTIA DSDQLPGYSV ETNILPTKMR
EKTPSYGKPR PLSMPADGNW MGIVDPFARP RGHGRKGEDA LCRYFSNERI PPIIEESSSP
PYRFSRPTTE RHLVRGADYI RGSRCYINSD LHSSATIPFQ EEGTKKKSGS SATKSSSTEP
SLLVSWFTRL KLLTH*

Mutated AA sequence

MEPVTKWSPK QVVDWTRGLD DCLQQYVHKF EREKINGEQL LQISHQDLEE LGVTRIGHQE
LVLEAVDLLC ALNYGLETDN MKNLVLKLRA SSHNLQNYIS SRRKSPAYDG NTSRKAPNEF
LTSVVELIGA AKALLAWLDR APFTGITDFS VTKNKIIQLC LDLTTTVQKD CFVAEMEDKV
LTVVKVLNGI CDKTIRSTTD PVMSQCACLE EVHLPNIKPG EGLGMYIKST YDGLHVITGT
TENSPADRSQ KIHAGDEVIQ VNQQTVVGWQ LKNLVKKLRE NPTGVVLLLK KRPTGSFNFT
PAPLKNLRWK PPLVQTSPPP ATTQSPESTM DTSLKKEKSA ILDLYIPPPP AVPYSPRDEN
GSFVYGGSSK CKQPLPGPKG SESPNSFLDQ ESRRRRFTIA DSDQLPGYSV ETNILPTKMR
EKTPSYGKPR PLSMPADGNW MGIVDPFARP RGHGRKGEDA LCRYFSNERI PPIIEESSSP
PYRFSRPTTE RHLVRGADYI RGSRCYINSD LHSSATIPLQ EEGTKKKSGS SATKSSSTEP
SLLVSWFTRL KLLTH*

Position of stopcodon in wt / mu CDS

1668 / 1668

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

556 / 556

Position of stopcodon in wt / mu cDNA

2239 / 2239

Position of start ATG in wt / mu cDNA

572 / 572

Last intron/exon boundary

1940

Theoretical NMD boundary in CDS

1318

Length of CDS

1668

Coding sequence (CDS) position

1557

cDNA position

2128

gDNA position

104221

Chromosomal position

154406465

Speed

0.36 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:

6:154406465G>T_3_ENST00000479339

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 96|4 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:154406465G>T (GRCh38)

Gene symbol

CNKSR3

Gene constraints

LOEUF: 0.68, LOF (oe): 0.46, misssense (oe): 0.93, synonymous (oe): 0.95 ? (gnomAD)

Ensembl transcript ID

ENST00000479339.5

Genbank transcript ID

NM_001368118 (by similarity), NM_001368119 (by similarity)

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.1317C>A
g.104221C>A

AA changes

AAE:	F439L	?
Score:	22

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs146307807
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	59	59

Protein conservation

Species	Match	AA	Alignment
Human		439	N	S	D	L	H	S	S	A	T	I	P	F	Q	E	E	G	T	K	K	K	S	G	S	S
mutated	not conserved	439	N	S	D	L	H	S	S	A	T	I	P	L	Q	E	E	G	T	K	K	K	S	G	S
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)	7.642	1
	2.263	1
(flanking)	5.25	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

6

Strand

-1

Original gDNA sequence snippet

AGCAGCGCCACGATTCCATTCCAGGAGGAAGGGACCAAAAA

Altered gDNA sequence snippet

AGCAGCGCCACGATTCCATTACAGGAGGAAGGGACCAAAAA

Original cDNA sequence snippet

AGCAGCGCCACGATTCCATTCCAGGAGGAAGGGACCAAAAA

Altered cDNA sequence snippet

AGCAGCGCCACGATTCCATTACAGGAGGAAGGGACCAAAAA

Wildtype AA sequence

MKNLVLKLRA SSHNLQNYIS SRRKSPAYDG NTSRKAPNEF LTSVVELIGA AKALLAWLDR
APFTGITDFS VTKNKIIQLC LDLTTTVQKD CFVAEMEDKV LTVVKVLNGI CDKTIRSTTD
PVMSQCACLE EVHLPNIKPG EGLGMYIKST YDGLHVITGT TENSPADRSQ KIHAGDEVIQ
VNQQTVVGWQ LKNLVKKLRE NPTGVVLLLK KRPTGSFNFT PAPLKNLRWK PPLVQTSPPP
ATTQSPESTM DTSLKKEKSA ILDLYIPPPP AVPYSPRDEN GSFVYGGSSK CKQPLPGPKG
SESPNSFLDQ ESRRRRFTIA DSDQLPGYSV ETNILPTKMR EKTPSYGKPR PLSMPADGNW
MGIVDPFARP RGHGRKGEDA LCRYFSNERI PPIIEESSSP PYRFSRPTTE RHLVRGADYI
RGSRCYINSD LHSSATIPFQ EEGTKKKSGS SATKSSSTEP SLLVSWFTRL KLLTH*

Mutated AA sequence

MKNLVLKLRA SSHNLQNYIS SRRKSPAYDG NTSRKAPNEF LTSVVELIGA AKALLAWLDR
APFTGITDFS VTKNKIIQLC LDLTTTVQKD CFVAEMEDKV LTVVKVLNGI CDKTIRSTTD
PVMSQCACLE EVHLPNIKPG EGLGMYIKST YDGLHVITGT TENSPADRSQ KIHAGDEVIQ
VNQQTVVGWQ LKNLVKKLRE NPTGVVLLLK KRPTGSFNFT PAPLKNLRWK PPLVQTSPPP
ATTQSPESTM DTSLKKEKSA ILDLYIPPPP AVPYSPRDEN GSFVYGGSSK CKQPLPGPKG
SESPNSFLDQ ESRRRRFTIA DSDQLPGYSV ETNILPTKMR EKTPSYGKPR PLSMPADGNW
MGIVDPFARP RGHGRKGEDA LCRYFSNERI PPIIEESSSP PYRFSRPTTE RHLVRGADYI
RGSRCYINSD LHSSATIPLQ EEGTKKKSGS SATKSSSTEP SLLVSWFTRL KLLTH*

Position of stopcodon in wt / mu CDS

1428 / 1428

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

476 / 476

Position of stopcodon in wt / mu cDNA

1779 / 1779

Position of start ATG in wt / mu cDNA

352 / 352

Last intron/exon boundary

1480

Theoretical NMD boundary in CDS

1078

Length of CDS

1428

Coding sequence (CDS) position

1317

cDNA position

1668

gDNA position

104221

Chromosomal position

154406465

Speed

0.50 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

Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

Back to summary table