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: ENST00000544301
Querying Taster for transcript #2: ENST00000224237
MT speed 0.12 s - this script 2.549754 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
ENST00000544301(MANE Select)	VIM	Deleterious	80\|20	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000224237	VIM	Deleterious	97\|3	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Protein features (might be) affected

MutationT@ster 2025

Variant:

10:17229708T>C_1_ENST00000544301

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 80|20 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr10:17229708T>C (GRCh38)

Gene symbol

VIM

Gene constraints

LOEUF: 0.54, LOF (oe): 0.36, misssense (oe): 0.91, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000544301.7

Genbank transcript ID

NM_003380 (exact from MANE)

UniProt / AlphaMissense peptide

VIME_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.286T>C
g.1468T>C

AA changes

AAE:	F96L	?
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 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L	Q
mutated	not conserved	96	D	F	S	L	A	D	A	I	N	T	E	L	K	N	T	R	T	N	E	K	V	E	L
Ptroglodytes	all identical	96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L
Mmulatta	all identical	96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L
Fcatus	all identical	96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L
Mmusculus	all identical	96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L
Ggallus	not conserved	217	E	-	-	-	-	D	V	D	N	A	S	L	A	R	L	D	L	E	R	K	V	ES	L
Trubripes	all identical	115	D	F	S	L	S	D	A	I	N	T	E	F	I	T	N	R	T	N	E	K	A	Q	M
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	all conserved	94	D	F	T	L	A	D	A	V	N	L	E	Y	K	A	N	R	T	N	E	K	A	E	M

Protein features

Start (aa)	End (aa)	Feature
2	466	CHAIN	lost
96	131	REGION	lost
96	131	COILED	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.839	1
	7.929	1
(flanking)	4.791	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

10

Strand

1

Original gDNA sequence snippet

CCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAAC

Altered gDNA sequence snippet

CCGACGCCATCAACACCGAGCTCAAGAACACCCGCACCAAC

Original cDNA sequence snippet

CCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAAC

Altered cDNA sequence snippet

CCGACGCCATCAACACCGAGCTCAAGAACACCCGCACCAAC

Wildtype AA sequence

MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV
YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE
DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE
AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS
LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE*

Mutated AA sequence

MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV
YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTELKNTR TNEKVELQEL NDRFANYIDK
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE
DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE
AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS
LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE*

Position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

Position of stopcodon in wt / mu cDNA

1832 / 1832

Position of start ATG in wt / mu cDNA

432 / 432

Last intron/exon boundary

1790

Theoretical NMD boundary in CDS

1308

Length of CDS

1401

Coding sequence (CDS) position

286

cDNA position

717

gDNA position

1468

Chromosomal position

17229708

Speed

0.07 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:

10:17229708T>C_2_ENST00000224237

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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

Chr10:17229708T>C (GRCh38)

Gene symbol

VIM

Gene constraints

LOEUF: 0.54, LOF (oe): 0.36, misssense (oe): 0.91, synonymous (oe): 1.02 ? (gnomAD)

Ensembl transcript ID

ENST00000224237.9

Genbank transcript ID

UniProt / AlphaMissense peptide

VIME_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.286T>C
g.1468T>C

AA changes

AAE:	F96L	?
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 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		96	D	F	S	L	A	D	A	I	N	T	E	F	K	N	T	R	T	N	E	K	V	E	L	Q
mutated	not conserved	96	D	F	S	L	A	D	A	I	N	T	E	L	K	N	T	R	T	N	E	K	V	E	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

Start (aa)	End (aa)	Feature
2	466	CHAIN	lost
96	131	REGION	lost
96	131	COILED	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	4.839	1
	7.929	1
(flanking)	4.791	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

10

Strand

1

Original gDNA sequence snippet

CCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAAC

Altered gDNA sequence snippet

CCGACGCCATCAACACCGAGCTCAAGAACACCCGCACCAAC

Original cDNA sequence snippet

CCGACGCCATCAACACCGAGTTCAAGAACACCCGCACCAAC

Altered cDNA sequence snippet

CCGACGCCATCAACACCGAGCTCAAGAACACCCGCACCAAC

Wildtype AA sequence

MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV
YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTEFKNTR TNEKVELQEL NDRFANYIDK
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE
DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE
AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS
LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE*

Mutated AA sequence

MSTRSVSSSS YRRMFGGPGT ASRPSSSRSY VTTSTRTYSL GSALRPSTSR SLYASSPGGV
YATRSSAVRL RSSVPGVRLL QDSVDFSLAD AINTELKNTR TNEKVELQEL NDRFANYIDK
VRFLEQQNKI LLAELEQLKG QGKSRLGDLY EEEMRELRRQ VDQLTNDKAR VEVERDNLAE
DIMRLREKLQ EEMLQREEAE NTLQSFRQDV DNASLARLDL ERKVESLQEE IAFLKKLHEE
EIQELQAQIQ EQHVQIDVDV SKPDLTAALR DVRQQYESVA AKNLQEAEEW YKSKFADLSE
AANRNNDALR QAKQESTEYR RQVQSLTCEV DALKGTNESL ERQMREMEEN FAVEAANYQD
TIGRLQDEIQ NMKEEMARHL REYQDLLNVK MALDIEIATY RKLLEGEESR ISLPLPNFSS
LNLRETNLDS LPLVDTHSKR TLLIKTVETR DGQVINETSQ HHDDLE*

Position of stopcodon in wt / mu CDS

1401 / 1401

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

467 / 467

Position of stopcodon in wt / mu cDNA

1546 / 1546

Position of start ATG in wt / mu cDNA

146 / 146

Last intron/exon boundary

1504

Theoretical NMD boundary in CDS

1308

Length of CDS

1401

Coding sequence (CDS) position

286

cDNA position

431

gDNA position

1468

Chromosomal position

17229708

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