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: ENST00000607772
Querying Taster for transcript #2: ENST00000673182
Querying Taster for transcript #3: ENST00000479339
MT speed 0.86 s - this script 3.238071 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
ENST00000607772(MANE Select)	CNKSR3	Deleterious	71\|29	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000479339	CNKSR3	Deleterious	73\|27	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed

Some transcripts had annotation problems and are not shown

MutationT@ster 2025

Variant:

6:154433494G>T_1_ENST00000607772

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 71|29 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:154433494G>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.521C>A
g.77192C>A

AA changes

AAE:	A174E	?
Score:	107

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375809234
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		174	L	T	T	T	V	Q	K	D	C	F	V	A	E	M	E	D	K	V	L	T	V	V	K	V
mutated	not conserved	174	L	T	T	T	V	Q	K	D	C	F	V	E	E	M	E	D	K	V
Ptroglodytes	all identical	174	L	T	T	T	V	Q	K	D	C	F	V	A	E	M	E	D	K	V
Mmulatta	all identical	174	L	T	T	T	V	Q	K	D	C	F	V	A	E	M	E	D	K	V
Fcatus	all identical	174	L	T	T	T	V	Q	K	D	C	L	V	A	E	M	E	D	K	V
Mmusculus	all identical	174	L	T	T	A	V	Q	K	D	C	L	I	A	E	M	E	D	K	V
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
80	174	DOMAIN	CRIC	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.314	0.267
	1.454	0.626
(flanking)	3.502	0.648

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

14

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

6

Strand

-1

Original gDNA sequence snippet

TCTTTAGGATTGCTTTGTAGCGGAAATGGAGGATAAAGTTT

Altered gDNA sequence snippet

TCTTTAGGATTGCTTTGTAGAGGAAATGGAGGATAAAGTTT

Original cDNA sequence snippet

CCAGAAGGATTGCTTTGTAGCGGAAATGGAGGATAAAGTTT

Altered cDNA sequence snippet

CCAGAAGGATTGCTTTGTAGAGGAAATGGAGGATAAAGTTT

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 CFVEEMEDKV
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*

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

521

cDNA position

1092

gDNA position

77192

Chromosomal position

154433494

Speed

0.44 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:

6:154433494G>T_3_ENST00000479339

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 73|27 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr6:154433494G>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.281C>A
g.77192C>A

AA changes

AAE:	A94E	?
Score:	107

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs375809234
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	0	1	1

Protein conservation

Species	Match	AA	Alignment
Human		94	L	T	T	T	V	Q	K	D	C	F	V	A	E	M	E	D	K	V	L	T	V	V	K	V
mutated	not conserved	94	L	T	T	T	V	Q	K	D	C	F	V	E	E	M	E	D	K	V	L	T	V	V	K
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)	-0.314	0.267
	1.454	0.626
(flanking)	3.502	0.648

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

14

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

6

Strand

-1

Original gDNA sequence snippet

TCTTTAGGATTGCTTTGTAGCGGAAATGGAGGATAAAGTTT

Altered gDNA sequence snippet

TCTTTAGGATTGCTTTGTAGAGGAAATGGAGGATAAAGTTT

Original cDNA sequence snippet

CCAGAAGGATTGCTTTGTAGCGGAAATGGAGGATAAAGTTT

Altered cDNA sequence snippet

CCAGAAGGATTGCTTTGTAGAGGAAATGGAGGATAAAGTTT

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 CFVEEMEDKV 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*

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

281

cDNA position

632

gDNA position

77192

Chromosomal position

154433494

Speed

0.42 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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Problem:

1

MutationT@ster 2025

Data problem

No NCBI gene ID found.

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