Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.901957741900338 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:39884583G>AN/A show variant in all transcripts   IGV
HGNC symbol HAP1
Ensembl transcript ID ENST00000341193
Genbank transcript ID NM_001079870
UniProt peptide P54257
alteration type single base exchange
alteration region CDS
DNA changes c.1094C>T
cDNA.1104C>T
g.6314C>T
AA changes S365L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 365
frameshift no
known variant Reference ID: rs4796693
databasehomozygous (A/A)heterozygousallele carriers
1000G15667402306
ExAC---
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6360.704
0.2680.718
(flanking)3.2770.748
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6313.5sequence motif lost- wt: ccca|GCGG
 mu: ccca.GTGG
Acc increased6304wt: 0.26 / mu: 0.37wt: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGC
mu: CAGGGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGC		 ctgc|CCTC
Acc marginally increased6313wt: 0.9164 / mu: 0.9182 (marginal change - not scored)wt: CCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATG
mu: CCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATG		 ccag|CGGA
Acc marginally increased6312wt: 0.9947 / mu: 0.9967 (marginal change - not scored)wt: ACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGAT
mu: ACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGAT		 ccca|GCGG
Acc marginally increased6316wt: 0.8703 / mu: 0.8861 (marginal change - not scored)wt: GTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGGCT
mu: GTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGGCT		 gcgg|AGGC
Acc marginally increased6307wt: 0.4322 / mu: 0.4417 (marginal change - not scored)wt: GGCTGACCTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAA
mu: GGCTGACCTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAA		 ccct|CCCC
Donor marginally increased6312wt: 0.9986 / mu: 0.9987 (marginal change - not scored)wt: TCCCCAGCGGAGGCC
mu: TCCCCAGTGGAGGCC		 CCCA|gcgg
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      365QMLILECVEQFSEASQQMAELSEV
mutated  not conserved    365VEQFLEASQQMAELSE
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000002132  346XXXXXXXXXXXEASQQMAELSE
Mmusculus  all identical  ENSMUSG00000006930  310LILECVEQFSEASQQMAELSE
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000074508  203QRLMMVCVDELTSANKQVVSLSE
Dmelanogaster  all conserved  FBgn0262872  418RQLMADISAQLNDANSQYDN
Celegans  not conserved  T27A3.1  232---LADKDKKERMISMEKEEMGA
Xtropicalis  all identical  ENSXETG00000012489  321SSLMLDCVEQFSEASRHVALLAE
protein features
start (aa)end (aa)featuredetails 
106461DOMAINHAP1 N-terminal.lost
261601COMPBIASGlu-rich.lost
573573CONFLICTP -> L (in Ref. 3; BAB13952).might get lost (downstream of altered splice site)
579579CONFLICTM -> V (in Ref. 1; AAC39861).might get lost (downstream of altered splice site)
611611CONFLICTA -> T (in Ref. 7; AAC50297).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1809 / 1809
position (AA) of stopcodon in wt / mu AA sequence 603 / 603
position of stopcodon in wt / mu cDNA 1819 / 1819
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 11 / 11
chromosome 17
strand -1
last intron/exon boundary 1366
theoretical NMD boundary in CDS 1305
length of CDS 1809
coding sequence (CDS) position 1094
cDNA position
(for ins/del: last normal base / first normal base)		 1104
gDNA position
(for ins/del: last normal base / first normal base)		 6314
chromosomal position
(for ins/del: last normal base / first normal base)		 39884583
original gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGCGGAGGCCAGCCAACAGATGG
altered gDNA sequence snippet CTGTCCTCTGCCCTCCCCAGTGGAGGCCAGCCAACAGATGG
original cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTCGGAGGCCAGCCAACAGATGG
altered cDNA sequence snippet GGAGTGTGTGGAGCAGTTTTTGGAGGCCAGCCAACAGATGG
wildtype AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEEVCTAFLI QLLPPVWESV TYGMVLQRER DLNTAARIGQ SLVKQNSVLM EENSKLEALL
GSAKEEILYL RHQVNLRDEL LQLYSDSDEE DEDEEEEEEE KEAEEEQEEE EAEEDLQCAH
PCDAPKLISQ EALLHQHHCP QLEALQEKLR LLEEENHQLR EEASQLDTLE DEEQMLILEC
VEQFSEASQQ MAELSEVLVL RLENYERQQQ EVARLQAQVL KLQQRCRMET LPGFQETLAE
ELRTSLRRMI SDPVYFMERN YEMPRGDTSS LRYDFRYSED REQVRGFEAE EGLMLAADIM
RGEDFTPAEE FVPQEELGAA KKVPAEEGVM EEAELVSEET EGWEEVELEL DEATRMNVVT
SALEASGLGP SHLDMNYVLQ QLANWQDAHY RRQLRWKMLQ KGECPHGALP AASRTSCRSS
CR*
mutated AA sequence MRPKRLGRCC AGSRLGPGDP AALTCAPSPS ASPAPEPSAQ PQARGTGQRV GSRATSGSQF
LSEARTGARP ASEAGAKAGA RRPSAFSAIQ GDVRSMPDNS DAPWTRFVFQ GPFGSRATGR
GTGKAAGIWK TPAAYVGRRP GVSGPERAAF IRELEEALCP NLPPPVKKIT QEDVKVMLYL
LEEVCTAFLI QLLPPVWESV TYGMVLQRER DLNTAARIGQ SLVKQNSVLM EENSKLEALL
GSAKEEILYL RHQVNLRDEL LQLYSDSDEE DEDEEEEEEE KEAEEEQEEE EAEEDLQCAH
PCDAPKLISQ EALLHQHHCP QLEALQEKLR LLEEENHQLR EEASQLDTLE DEEQMLILEC
VEQFLEASQQ MAELSEVLVL RLENYERQQQ EVARLQAQVL KLQQRCRMET LPGFQETLAE
ELRTSLRRMI SDPVYFMERN YEMPRGDTSS LRYDFRYSED REQVRGFEAE EGLMLAADIM
RGEDFTPAEE FVPQEELGAA KKVPAEEGVM EEAELVSEET EGWEEVELEL DEATRMNVVT
SALEASGLGP SHLDMNYVLQ QLANWQDAHY RRQLRWKMLQ KGECPHGALP AASRTSCRSS
CR*
speed 1.01 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