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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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000585101
Querying Taster for transcript #2: ENST00000474627
MT speed 0 s - this script 4.327821 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATPAF2disease_causing_automatic0.999999999975598simple_aaeaffected0W94Rsingle base exchangers104894554show file
ATPAF2disease_causing_automatic1without_aaeaffected0single base exchangers104894554show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999975598 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM040214)
  • known disease mutation: rs1995 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:17931590A>TN/A show variant in all transcripts   IGV
HGNC symbol ATPAF2
Ensembl transcript ID ENST00000474627
Genbank transcript ID NM_145691
UniProt peptide Q8N5M1
alteration type single base exchange
alteration region CDS
DNA changes c.280T>A
cDNA.435T>A
g.10934T>A
AA changes W94R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
94
frameshift no
known variant Reference ID: rs104894554
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1995 (pathogenic for Nuclearly-encoded mitochondrial complex V (ATP synthase) deficiency 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0611
5.0051
(flanking)-0.1530.935
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained109340.58mu: CTGAGAGGGATTCCC GAGA|ggga
Donor gained109300.93mu: GCTACTGAGAGGGAT TACT|gaga
Donor gained109290.31mu: GGCTACTGAGAGGGA CTAC|tgag
distance from splice site 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      94SEALAIAVATEWDSQQDTIKYYTM
mutated  not conserved    94SEALAIAVATERDSQQDTIKYYT
Ptroglodytes  all identical  ENSPTRG00000008840  94SEALAIAVATEWDSQQDTIKYYT
Mmulatta  all identical  ENSMMUG00000003657  94SEALAIAVATEWDSQQDTIKYYT
Fcatus  all identical  ENSFCAG00000001987  94SEALAIAVATEWDSQQDTIKFYT
Mmusculus  all identical  ENSMUSG00000042709  103SEALAIAVATEWDSQQDTIKFYT
Ggallus  all identical  ENSGALG00000004926  86SEALAIAVATEWDSQKDTIKFYT
Trubripes  all identical  ENSTRUG00000016869  50NEALAIAVATEWDAQKDTLKF
Drerio  all identical  ENSDARG00000056270  95NEALAIAVANEWD
Dmelanogaster  all conserved  FBgn0021856  85LAIAVATEFDAQKENIERSR
Celegans  all identical  Y116A8C.27  71SYPLALAIAEEWSSQ
Xtropicalis  all identical  ENSXETG00000012153  82SEALAVAVATEWDCQRDV
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 870 / 870
position (AA) of stopcodon in wt / mu AA sequence 290 / 290
position of stopcodon in wt / mu cDNA 1025 / 1025
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 156 / 156
chromosome 17
strand -1
last intron/exon boundary 888
theoretical NMD boundary in CDS 682
length of CDS 870
coding sequence (CDS) position 280
cDNA position
(for ins/del: last normal base / first normal base)
435
gDNA position
(for ins/del: last normal base / first normal base)
10934
chromosomal position
(for ins/del: last normal base / first normal base)
17931590
original gDNA sequence snippet CCATTGCAGTGGCTACTGAGTGGGATTCCCAGCAGGATACC
altered gDNA sequence snippet CCATTGCAGTGGCTACTGAGAGGGATTCCCAGCAGGATACC
original cDNA sequence snippet CCATTGCAGTGGCTACTGAGTGGGATTCCCAGCAGGATACC
altered cDNA sequence snippet CCATTGCAGTGGCTACTGAGAGGGATTCCCAGCAGGATACC
wildtype AA sequence MWRSCLRLRD GGRRLLNRPA GGPSASMSPG PTIPSPARAY APPTERKRFY QNVSITQGEG
GFEINLDHRK LKTPQAKLFT VPSEALAIAV ATEWDSQQDT IKYYTMHLTT LCNTSLDNPT
QRNKDQLIRA AVKFLDTDTI CYRVEEPETL VELQRNEWDP IIEWAEKRYG VEISSSTSIM
GPSIPAKTRE VLVSHLASYN TWALQGIEFV AAQLKSMVLT LGLIDLRLTV EQAVLLSRLE
EEYQIQKWGN IEWAHDYELQ ELRARTAAGT LFIHLCSEST TVKHKLLKE*
mutated AA sequence MWRSCLRLRD GGRRLLNRPA GGPSASMSPG PTIPSPARAY APPTERKRFY QNVSITQGEG
GFEINLDHRK LKTPQAKLFT VPSEALAIAV ATERDSQQDT IKYYTMHLTT LCNTSLDNPT
QRNKDQLIRA AVKFLDTDTI CYRVEEPETL VELQRNEWDP IIEWAEKRYG VEISSSTSIM
GPSIPAKTRE VLVSHLASYN TWALQGIEFV AAQLKSMVLT LGLIDLRLTV EQAVLLSRLE
EEYQIQKWGN IEWAHDYELQ ELRARTAAGT LFIHLCSEST TVKHKLLKE*
speed 1.35 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM040214)
  • known disease mutation: rs1995 (pathogenic)
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:17931590A>TN/A show variant in all transcripts   IGV
HGNC symbol ATPAF2
Ensembl transcript ID ENST00000585101
Genbank transcript ID N/A
UniProt peptide Q8N5M1
alteration type single base exchange
alteration region intron
DNA changes g.10934T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs104894554
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs1995 (pathogenic for Nuclearly-encoded mitochondrial complex V (ATP synthase) deficiency 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)

known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)
known disease mutation at this position, please check HGMD for details (HGMD ID CM040214)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0611
5.0051
(flanking)-0.1530.935
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained109340.58mu: CTGAGAGGGATTCCC GAGA|ggga
Donor gained109300.93mu: GCTACTGAGAGGGAT TACT|gaga
Donor gained109290.31mu: GGCTACTGAGAGGGA CTAC|tgag
distance from splice site 339
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features no protein features affected
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 156 / 156
chromosome 17
strand -1
last intron/exon boundary 513
theoretical NMD boundary in CDS 307
length of CDS 324
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
10934
chromosomal position
(for ins/del: last normal base / first normal base)
17931590
original gDNA sequence snippet CCATTGCAGTGGCTACTGAGTGGGATTCCCAGCAGGATACC
altered gDNA sequence snippet CCATTGCAGTGGCTACTGAGAGGGATTCCCAGCAGGATACC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MWRSCLRLRD GGRRLLNRPA GGPSASMSPG PTIPSPARAY APPTERKRFY QNVSITQGED
HIVQHIIGQP NPEKQGSADP GSREVSGHRH HLLQGGGARD ISGTSKE*
mutated AA sequence N/A
speed 1.04 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