MutationTaster - study a chromosomal position

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...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000234396
Querying Taster for transcript #2: ENST00000412314
Querying Taster for transcript #3: ENST00000432098
MT speed 0 s - this script 3.088531 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP6V1B1	disease_causing_automatic	0.999999999990307	simple_aae			0	L81P	single base exchange	rs121964880		show file
ATP6V1B1	disease_causing_automatic	0.999999999990307	simple_aae			0	L81P	single base exchange	rs121964880		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999990307 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990267)
known disease mutation: rs12228 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:71185243T>CN/A show variant in all transcripts IGV

HGNC symbol

ATP6V1B1

Ensembl transcript ID

ENST00000234396

Genbank transcript ID

NM_001692

UniProt peptide

P15313

alteration type

single base exchange

alteration region

CDS

DNA changes

c.242T>C
cDNA.315T>C
g.22232T>C

AA changes

L81P Score: 98 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

Reference ID: rs121964880
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs12228 (pathogenic for Nephrolithiasis|Nephrocalcinosis|Renal tubular acidosis with progressive nerve deafness) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990267)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990267)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990267)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.226	1
	4.318	1
(flanking)	-0.296	0.962

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000012038

Mmulatta

all identical

ENSMMUG00000002090

Fcatus

not conserved

ENSFCAG00000013451

Mmusculus

all identical

ENSMUSG00000006269

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0005671

Celegans

all identical

F20B6.2

Xtropicalis

all identical

ENSXETG00000021532

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1542 / 1542

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

514 / 514

position of stopcodon in wt / mu cDNA

1615 / 1615

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

74 / 74

chromosome

strand

last intron/exon boundary

1452

theoretical NMD boundary in CDS

1328

length of CDS

1542

coding sequence (CDS) position

242

cDNA position
(for ins/del: last normal base / first normal base)

315

gDNA position
(for ins/del: last normal base / first normal base)

22232

chromosomal position
(for ins/del: last normal base / first normal base)

71185243

original gDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCTTGAGGTGGCTGGCACCAAGG

altered gDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCCTGAGGTGGCTGGCACCAAGG

original cDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCTTGAGGTGGCTGGCACCAAGG

altered cDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCCTGAGGTGGCTGGCACCAAGG

wildtype AA sequence

MAMEIDSRPG GLPGSSCNLG AAREHMQAVT RNYITHPRVT YRTVCSVNGP LVVLDRVKFA
QYAEIVHFTL PDGTQRSGQV LEVAGTKAIV QVFEGTSGID ARKTTCEFTG DILRTPVSED
MLGRVFNGSG KPIDKGPVVM AEDFLDINGQ PINPHSRIYP EEMIQTGISP IDVMNSIARG
QKIPIFSAAG LPHNEIAAQI CRQAGLVKKS KAVLDYHDDN FAIVFAAMGV NMETARFFKS
DFEQNGTMGN VCLFLNLAND PTIERIITPR LALTTAEFLA YQCEKHVLVI LTDMSSYAEA
LREVSAAREE VPGRRGFPGY MYTDLATIYE RAGRVEGRGG SITQIPILTM PNDDITHPIP
DLTGFITEGQ IYVDRQLHNR QIYPPINVLP SLSRLMKSAI GEGMTRKDHG DVSNQLYACY
AIGKDVQAMK AVVGEEALTS EDLLYLEFLQ KFEKNFINQG PYENRSVFES LDLGWKLLRI
FPKEMLKRIP QAVIDEFYSR EGALQDLAPD TAL*

mutated AA sequence

MAMEIDSRPG GLPGSSCNLG AAREHMQAVT RNYITHPRVT YRTVCSVNGP LVVLDRVKFA
QYAEIVHFTL PDGTQRSGQV PEVAGTKAIV QVFEGTSGID ARKTTCEFTG DILRTPVSED
MLGRVFNGSG KPIDKGPVVM AEDFLDINGQ PINPHSRIYP EEMIQTGISP IDVMNSIARG
QKIPIFSAAG LPHNEIAAQI CRQAGLVKKS KAVLDYHDDN FAIVFAAMGV NMETARFFKS
DFEQNGTMGN VCLFLNLAND PTIERIITPR LALTTAEFLA YQCEKHVLVI LTDMSSYAEA
LREVSAAREE VPGRRGFPGY MYTDLATIYE RAGRVEGRGG SITQIPILTM PNDDITHPIP
DLTGFITEGQ IYVDRQLHNR QIYPPINVLP SLSRLMKSAI GEGMTRKDHG DVSNQLYACY
AIGKDVQAMK AVVGEEALTS EDLLYLEFLQ KFEKNFINQG PYENRSVFES LDLGWKLLRI
FPKEMLKRIP QAVIDEFYSR EGALQDLAPD TAL*

speed

0.22 s

All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999990307 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM990267)
known disease mutation: rs12228 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:71185243T>CN/A show variant in all transcripts IGV

HGNC symbol

ATP6V1B1

Ensembl transcript ID

ENST00000412314

Genbank transcript ID

N/A

UniProt peptide

P15313

alteration type

single base exchange

alteration region

CDS

DNA changes

c.242T>C
cDNA.276T>C
g.22232T>C

AA changes

L81P Score: 98 explain score(s)

position(s) of altered AA
if AA alteration in CDS

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.226	1
	4.318	1
(flanking)	-0.296	0.962

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000012038

Mmulatta

all identical

ENSMMUG00000002090

Fcatus

not conserved

ENSFCAG00000013451

Mmusculus

all identical

ENSMUSG00000006269

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0005671

Celegans

all identical

F20B6.2

Xtropicalis

all identical

ENSXETG00000021532

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1491 / 1491

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

497 / 497

position of stopcodon in wt / mu cDNA

1525 / 1525

poly(A) signal

N/A

conservation
nucleotide level for all changes - no scoring up to now

N/A

position of start ATG in wt / mu cDNA

35 / 35

chromosome

strand

last intron/exon boundary

1362

theoretical NMD boundary in CDS

1277

length of CDS

1491

coding sequence (CDS) position

242

cDNA position
(for ins/del: last normal base / first normal base)

276

gDNA position
(for ins/del: last normal base / first normal base)

22232

chromosomal position
(for ins/del: last normal base / first normal base)

71185243

original gDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCTTGAGGTGGCTGGCACCAAGG

altered gDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCCTGAGGTGGCTGGCACCAAGG

original cDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCTTGAGGTGGCTGGCACCAAGG

altered cDNA sequence snippet

TCAGAGGAGCGGGCAGGTGCCTGAGGTGGCTGGCACCAAGG

wildtype AA sequence

MAMEIDSRPG GLPGSSCNLG AAREHMQAVT RNYITHPRVT YRTVCSVNGP LVVLDRVKFA
QYAEIVHFTL PDGTQRSGQV LEVAGTKAIV QVFEGTSGID ARKTTCEFTG DILRTPVSED
MLGRVFNGSG KPIDKGPVVM AEDFLDINGQ PINPHSRIYP EEMIQTGISP IDVMNSIARG
QKIPIFSAAG LPHNEIAAQI CRQAGLVKKS KAVLDYHDDN FAIVFAAMGV NMETARFFKS
DFEQNGTMGN VCLFLNLAND PTIERIITPR LALTTAEFLA YQCEKHVLVI LTDMSSYAEA
LREVSAAREE VPGRRGFPGY MYTDLATIYE RAGRVEDITH PIPDLTGFIT EGQIYVDRQL
HNRQIYPPIN VLPSLSRLMK SAIGEGMTRK DHGDVSNQLY ACYAIGKDVQ AMKAVVGEEA
LTSEDLLYLE FLQKFEKNFI NQGPYENRSV FESLDLGWKL LRIFPKEMLK RIPQAVIDEF
YSREGALQDL APDTAL*

mutated AA sequence

MAMEIDSRPG GLPGSSCNLG AAREHMQAVT RNYITHPRVT YRTVCSVNGP LVVLDRVKFA
QYAEIVHFTL PDGTQRSGQV PEVAGTKAIV QVFEGTSGID ARKTTCEFTG DILRTPVSED
MLGRVFNGSG KPIDKGPVVM AEDFLDINGQ PINPHSRIYP EEMIQTGISP IDVMNSIARG
QKIPIFSAAG LPHNEIAAQI CRQAGLVKKS KAVLDYHDDN FAIVFAAMGV NMETARFFKS
DFEQNGTMGN VCLFLNLAND PTIERIITPR LALTTAEFLA YQCEKHVLVI LTDMSSYAEA
LREVSAAREE VPGRRGFPGY MYTDLATIYE RAGRVEDITH PIPDLTGFIT EGQIYVDRQL
HNRQIYPPIN VLPSLSRLMK SAIGEGMTRK DHGDVSNQLY ACYAIGKDVQ AMKAVVGEEA
LTSEDLLYLE FLQKFEKNFI NQGPYENRSV FESLDLGWKL LRIFPKEMLK RIPQAVIDEF
YSREGALQDL APDTAL*

speed

1.16 s

Problems

annotation problem

The chosen transcript ENST00000432098 on chromosome 2 has no correct in-frame stop codon (TGA, TAA or TAG) annotated
This is likely to cause a false prediction. You should choose another transcript.

back to results table