Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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 3.1 s - this script 9.382827 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATP6V1B1disease_causing_automatic0.999999948505695simple_aaeaffected0G78Rsingle base exchangers121964881show file
ATP6V1B1disease_causing_automatic0.999999948505695simple_aaeaffected0G78Rsingle base exchangers121964881show file

some transcripts had annotation problems and are not shown

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999948505695 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030199)
  • known disease mutation: rs12229 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:71185233G>AN/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.232G>A
cDNA.305G>A
g.22222G>A
AA changes G78R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
78
frameshift no
known variant Reference ID: rs121964881
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs12229 (pathogenic for Renal tubular acidosis with progressive nerve deafness|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)
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
PhyloPPhastCons
(flanking)-0.7810.804
5.2261
(flanking)5.2261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased22222wt: 0.9364 / mu: 0.9855 (marginal change - not scored)wt: GGAGCGGGCAGGTGC
mu: GGAGCAGGCAGGTGC
 AGCG|ggca
Donor marginally increased22214wt: 0.9961 / mu: 0.9972 (marginal change - not scored)wt: GACTCAGAGGAGCGG
mu: GACTCAGAGGAGCAG
 CTCA|gagg
Donor increased22226wt: 0.46 / mu: 0.56wt: CGGGCAGGTGCTTGA
mu: CAGGCAGGTGCTTGA
 GGCA|ggtg
Donor gained222170.41mu: TCAGAGGAGCAGGCA AGAG|gagc
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78HFTLPDGTQRSGQVLEVAGTKAIV
mutated  not conserved    78HFTLPDGTQRSRQVLEVAGTKAI
Ptroglodytes  all identical  ENSPTRG00000012038  78HFTLPDGTQRSGQVLEVAGTKAI
Mmulatta  all identical  ENSMMUG00000002090  78HFTLPDGTQRSGQVLEVAGTKAI
Fcatus  not conserved  ENSFCAG00000013451  78NFTLPXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000006269  78NFTLPDGTQRSGQVLEVAGTKAI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0005671  63QLRLADGTVRSGQV
Celegans  all identical  F20B6.2  66KITLPDGSKRSGQVLEIS
Xtropicalis  all identical  ENSXETG00000021532  69TSRSGQILEVSGSKAI
protein features
start (aa)end (aa)featuredetails 
467467CONFLICTV -> M (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
474474CONFLICTG -> S (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
503503CONFLICTA -> R (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
510513MOTIFPDZ-binding.might get lost (downstream of altered splice site)
513513MUTAGENL->G: Loss of interactions with SLC9A3R1 and SCL4A7.might get lost (downstream of altered splice site)
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 2
strand 1
last intron/exon boundary 1452
theoretical NMD boundary in CDS 1328
length of CDS 1542
coding sequence (CDS) position 232
cDNA position
(for ins/del: last normal base / first normal base)
305
gDNA position
(for ins/del: last normal base / first normal base)
22222
chromosomal position
(for ins/del: last normal base / first normal base)
71185233
original gDNA sequence snippet CAGATGGGACTCAGAGGAGCGGGCAGGTGCTTGAGGTGGCT
altered gDNA sequence snippet CAGATGGGACTCAGAGGAGCAGGCAGGTGCTTGAGGTGGCT
original cDNA sequence snippet CAGATGGGACTCAGAGGAGCGGGCAGGTGCTTGAGGTGGCT
altered cDNA sequence snippet CAGATGGGACTCAGAGGAGCAGGCAGGTGCTTGAGGTGGCT
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 PDGTQRSRQV 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*
speed 1.50 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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999948505695 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030199)
  • known disease mutation: rs12229 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:71185233G>AN/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.232G>A
cDNA.266G>A
g.22222G>A
AA changes G78R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
78
frameshift no
known variant Reference ID: rs121964881
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs12229 (pathogenic for Renal tubular acidosis with progressive nerve deafness|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030199)
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
PhyloPPhastCons
(flanking)-0.7810.804
5.2261
(flanking)5.2261
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased22222wt: 0.9364 / mu: 0.9855 (marginal change - not scored)wt: GGAGCGGGCAGGTGC
mu: GGAGCAGGCAGGTGC
 AGCG|ggca
Donor marginally increased22214wt: 0.9961 / mu: 0.9972 (marginal change - not scored)wt: GACTCAGAGGAGCGG
mu: GACTCAGAGGAGCAG
 CTCA|gagg
Donor increased22226wt: 0.46 / mu: 0.56wt: CGGGCAGGTGCTTGA
mu: CAGGCAGGTGCTTGA
 GGCA|ggtg
Donor gained222170.41mu: TCAGAGGAGCAGGCA AGAG|gagc
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      78HFTLPDGTQRSGQVLEVAGTKAIV
mutated  not conserved    78HFTLPDGTQRSRQVLEVAGTKAI
Ptroglodytes  all identical  ENSPTRG00000012038  78HFTLPDGTQRSGQVLEVAGTKAI
Mmulatta  all identical  ENSMMUG00000002090  78HFTLPDGTQRSGQVLEVAGTKAI
Fcatus  not conserved  ENSFCAG00000013451  78NFTLPXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000006269  78NFTLPDGTQRSGQVLEVAGTKAI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0005671  63QLRLADGTVRSGQV
Celegans  all identical  F20B6.2  66KITLPDGSKRSGQVLEIS
Xtropicalis  all identical  ENSXETG00000021532  69TSRSGQILEVSGSKAI
protein features
start (aa)end (aa)featuredetails 
467467CONFLICTV -> M (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
474474CONFLICTG -> S (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
503503CONFLICTA -> R (in Ref. 1; AAA36498).might get lost (downstream of altered splice site)
510513MOTIFPDZ-binding.might get lost (downstream of altered splice site)
513513MUTAGENL->G: Loss of interactions with SLC9A3R1 and SCL4A7.might get lost (downstream of altered splice site)
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 2
strand 1
last intron/exon boundary 1362
theoretical NMD boundary in CDS 1277
length of CDS 1491
coding sequence (CDS) position 232
cDNA position
(for ins/del: last normal base / first normal base)
266
gDNA position
(for ins/del: last normal base / first normal base)
22222
chromosomal position
(for ins/del: last normal base / first normal base)
71185233
original gDNA sequence snippet CAGATGGGACTCAGAGGAGCGGGCAGGTGCTTGAGGTGGCT
altered gDNA sequence snippet CAGATGGGACTCAGAGGAGCAGGCAGGTGCTTGAGGTGGCT
original cDNA sequence snippet CAGATGGGACTCAGAGGAGCGGGCAGGTGCTTGAGGTGGCT
altered cDNA sequence snippet CAGATGGGACTCAGAGGAGCAGGCAGGTGCTTGAGGTGGCT
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 PDGTQRSRQV 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*
speed 1.60 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

Problems

annotation problem

back to results table