Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999740836456851 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM023023)
  • known disease mutation: rs5159 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr7:138394378C>TN/A show variant in all transcripts   IGV
HGNC symbol ATP6V0A4
Ensembl transcript ID ENST00000393054
Genbank transcript ID NM_130841
UniProt peptide Q9HBG4
alteration type single base exchange
alteration region CDS
DNA changes c.2420G>A
cDNA.2658G>A
g.89928G>A
AA changes R807Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 807
frameshift no
known variant Reference ID: rs28939081
databasehomozygous (T/T)heterozygousallele carriers
1000G011
ExAC022

known disease mutation: rs5159 (pathogenic for Renal tubular acidosis, distal, autosomal recessive) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023023)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.3340.016
3.4820.742
(flanking)0.5030.723
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased89918wt: 0.9741 / mu: 0.9784 (marginal change - not scored)wt: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCGACTGCACTGG
mu: AGGGCCTCTCTGCTTTCCTGCACGCCCTGCAACTGCACTGG		 ctgc|ACGC
Donor gained899240.30mu: ACGCCCTGCAACTGC GCCC|tgca
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      807MEGLSAFLHALRLHWVEFQNKFYV
mutated  all conserved    807MEGLSAFLHALQLHWVEFQNKFY
Ptroglodytes  all identical  ENSPTRG00000019746  807MEGLSAFLHALRLHWVEFQNKFY
Mmulatta  all identical  ENSMMUG00000006547  806MEGLSAFLHALRLHWVEFQNKFY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038600  800MEGLSAFLHALRLHWVEFQNKFY
Ggallus  all identical  ENSGALG00000012810  804MEGLSAFLHALRLHWVEFQNKFY
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0028671  819MEGLSAFLHTLRLHWVEFQSKFY
Celegans  all identical  ZK637.8  868MEGLSAFLHALRLHWVEFQSKFY
Xtropicalis  all identical  ENSXETG00000011571  805MEGLSAFLHALRLHWVEFQNKFY
protein features
start (aa)end (aa)featuredetails 
774812TRANSMEMHelical; (Potential).lost
813840TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2523 / 2523
position (AA) of stopcodon in wt / mu AA sequence 841 / 841
position of stopcodon in wt / mu cDNA 2761 / 2761
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 239 / 239
chromosome 7
strand -1
last intron/exon boundary 2668
theoretical NMD boundary in CDS 2379
length of CDS 2523
coding sequence (CDS) position 2420
cDNA position
(for ins/del: last normal base / first normal base)		 2658
gDNA position
(for ins/del: last normal base / first normal base)		 89928
chromosomal position
(for ins/del: last normal base / first normal base)		 138394378
original gDNA sequence snippet TGCTTTCCTGCACGCCCTGCGACTGCACTGGTAAGGATGGT
altered gDNA sequence snippet TGCTTTCCTGCACGCCCTGCAACTGCACTGGTAAGGATGGT
original cDNA sequence snippet TGCTTTCCTGCACGCCCTGCGACTGCACTGGGTTGAGTTCC
altered cDNA sequence snippet TGCTTTCCTGCACGCCCTGCAACTGCACTGGGTTGAGTTCC
wildtype AA sequence MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDPIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALRLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*
mutated AA sequence MVSVFRSEEM CLSQLFLQVE AAYCCVAELG ELGLVQFKDL NMNVNSFQRK FVNEVRRCES
LERILRFLED EMQNEIVVQL LEKSPLTPLP REMITLETVL EKLEGELQEA NQNQQALKQS
FLELTELKYL LKKTQDFFET ETNLADDFFT EDTSGLLELK AVPAYMTGKL GFIAGVINRE
RMASFERLLW RICRGNVYLK FSEMDAPLED PVTKEEIQKN IFIIFYQGEQ LRQKIKKICD
GFRATVYPCP EPAVERREML ESVNVRLEDL ITVITQTESH RQRLLQEAAA NWHSWLIKVQ
KMKAVYHILN MCNIDVTQQC VIAEIWFPVA DATRIKRALE QGMELSGSSM APIMTTVQSK
TAPPTFNRTN KFTAGFQNIV DAYGVGSYRE INPAPYTIIT FPFLFAVMFG DCGHGTVMLL
AALWMILNER RLLSQKTDNE IWNTFFHGRY LILLMGIFSI YTGLIYNDCF SKSLNIFGSS
WSVQPMFRNG TWNTHVMEES LYLQLDPAIP GVYFGNPYPF GIDPIWNLAS NKLTFLNSYK
MKMSVILGIV QMVFGVILSL FNHIYFRRTL NIILQFIPEM IFILCLFGYL VFMIIFKWCC
FDVHVSQHAP SILIHFINMF LFNYSDSSNA PLYKHQQEVQ SFFVVMALIS VPWMLLIKPF
ILRASHRKSQ LQASRIQEDA TENIEGDSSS PSSRSGQRTS ADTHGALDDH GEEFNFGDVF
VHQAIHTIEY CLGCISNTAS YLRLWALSLA HAQLSEVLWT MVMNSGLQTR GWGGIVGVFI
IFAVFAVLTV AILLIMEGLS AFLHALQLHW VEFQNKFYVG DGYKFSPFSF KHILDGTAEE
*
speed 1.33 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