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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000282561
MT speed 0 s - this script 2.381531 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJA1disease_causing_automatic0.999999988949647simple_aaeaffected0G143Ssingle base exchangers28931600show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999988949647 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040076)
  • known disease mutation: rs16987 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:121768420G>AN/A show variant in all transcripts   IGV
HGNC symbol GJA1
Ensembl transcript ID ENST00000282561
Genbank transcript ID NM_000165
UniProt peptide P17302
alteration type single base exchange
alteration region CDS
DNA changes c.427G>A
cDNA.584G>A
g.11583G>A
AA changes G143S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 143
frameshift no
known variant Reference ID: rs28931600
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16987 (pathogenic for Syndactyly type 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040076)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040076)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040076)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8750.312
6.0491
(flanking)4.4191
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 increased11588wt: 0.8923 / mu: 0.9089 (marginal change - not scored)wt: GGTAAGGTGAAAATG
mu: AGTAAGGTGAAAATG		 TAAG|gtga
Donor marginally increased11578wt: 0.9403 / mu: 0.9966 (marginal change - not scored)wt: TGAAGAGCATGGTAA
mu: TGAAGAGCATAGTAA		 AAGA|gcat
Donor marginally increased11583wt: 0.9805 / mu: 0.9948 (marginal change - not scored)wt: AGCATGGTAAGGTGA
mu: AGCATAGTAAGGTGA		 CATG|gtaa
Donor increased11587wt: 0.21 / mu: 0.32wt: TGGTAAGGTGAAAAT
mu: TAGTAAGGTGAAAAT		 GTAA|ggtg
distance from splice site 443
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      143IKKFKYGIEEHGKVKMRGGLLRTY
mutated  not conserved    143IKKFKYGIEEHSKVKMRGGLLRT
Ptroglodytes  all identical  ENSPTRG00000018560  143IKKFKYGIEEHGKVKMRGGLLRT
Mmulatta  all identical  ENSMMUG00000005225  143IKKFKYGIEEHGKVKMRGGLLRT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000050953  143IKKFKYGIEEHGKVKMRGGLLRT
Ggallus  all identical  ENSGALG00000014873  143IKKFKYGIEEHGKVKMRGGLLRT
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000041799  143LKKFKHGLEEHGKVKMKGSLLRT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025411  143IKKFKYGLEEHGKVKMRGGLLRT
protein features
start (aa)end (aa)featuredetails 
100154TOPO_DOMCytoplasmic (Potential).lost
155177TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
178208TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
192192DISULFIDmight get lost (downstream of altered splice site)
198198DISULFIDmight get lost (downstream of altered splice site)
209231TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
232382TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
240242HELIXmight get lost (downstream of altered splice site)
246253HELIXmight get lost (downstream of altered splice site)
247247MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
255257HELIXmight get lost (downstream of altered splice site)
262262MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
313313MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
314314MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
325325MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
326326MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
328328MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
330330MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
365365MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
368368MOD_RESPhosphoserine; by PKC/PRKCG (By similarity).might get lost (downstream of altered splice site)
369369MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
373373MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1149 / 1149
position (AA) of stopcodon in wt / mu AA sequence 383 / 383
position of stopcodon in wt / mu cDNA 1306 / 1306
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 158 / 158
chromosome 6
strand 1
last intron/exon boundary 142
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1149
coding sequence (CDS) position 427
cDNA position
(for ins/del: last normal base / first normal base)		 584
gDNA position
(for ins/del: last normal base / first normal base)		 11583
chromosomal position
(for ins/del: last normal base / first normal base)		 121768420
original gDNA sequence snippet AGTACGGTATTGAAGAGCATGGTAAGGTGAAAATGCGAGGG
altered gDNA sequence snippet AGTACGGTATTGAAGAGCATAGTAAGGTGAAAATGCGAGGG
original cDNA sequence snippet AGTACGGTATTGAAGAGCATGGTAAGGTGAAAATGCGAGGG
altered cDNA sequence snippet AGTACGGTATTGAAGAGCATAGTAAGGTGAAAATGCGAGGG
wildtype AA sequence MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*
mutated AA sequence MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHSKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*
speed 0.30 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
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