Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999963493247008 (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) chr3:125865766C>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH1L1
Ensembl transcript ID ENST00000273450
Genbank transcript ID NM_001270364
UniProt peptide O75891
alteration type single base exchange
alteration region CDS
DNA changes c.1018G>T
cDNA.1236G>T
g.51072G>T
AA changes V340F Score: 50 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 340
frameshift no
known variant Reference ID: rs2886059
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC18521594217794
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6260.349
0.9530.355
(flanking)-0.2210.347
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 increased51069wt: 0.2705 / mu: 0.3236 (marginal change - not scored)wt: CATCAGGTCTTGCTTTGCAGAGTGTTTGGCAGCGGATCCTC
mu: CATCAGGTCTTGCTTTGCAGAGTTTTTGGCAGCGGATCCTC		 caga|GTGT
Donor increased51076wt: 0.51 / mu: 0.67wt: TGTTTGGCAGCGGAT
mu: TTTTTGGCAGCGGAT		 TTTG|gcag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      340AELVTAEAVRSVWQRILPKVLEVE
mutated  not conserved    340AELVTAEAVRSFWQRILPKVLEV
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000012488  332AELVTAEAVRSAWQRILPNVLEV
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000030088  330EELATAEAVRSSWMRILPNVPEV
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006080  330EEGRFAEQMRAVWQSILSNVSRI
Drerio  all identical  ENSDARG00000077004  332DENRFAEQMRVVWKSILTNVEKI
Dmelanogaster  all conserved  FBgn0032945  341DELVKRSLLAGIWKAILKE--DV
Celegans  all conserved  F36H1.6  340EEKSTVAKLKKIWTGILKT--QV
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
323392DOMAINAcyl carrier.lost
347351HELIXmight get lost (downstream of altered splice site)
354354MOD_RESO-(pantetheine 4'-phosphoryl)serine (By similarity).might get lost (downstream of altered splice site)
356367HELIXmight get lost (downstream of altered splice site)
375380HELIXmight get lost (downstream of altered splice site)
384397HELIXmight get lost (downstream of altered splice site)
417902REGIONAldehyde dehydrogenase.might get lost (downstream of altered splice site)
470470CONFLICTD -> G (in Ref. 1; AAC35000).might get lost (downstream of altered splice site)
571573NP_BINDNADP (By similarity).might get lost (downstream of altered splice site)
597600NP_BINDNADP (By similarity).might get lost (downstream of altered splice site)
613613MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
630635NP_BINDNADP (By similarity).might get lost (downstream of altered splice site)
650651NP_BINDNADP (By similarity).might get lost (downstream of altered splice site)
673673ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
677677CONFLICTK -> E (in Ref. 1; AAC35000).might get lost (downstream of altered splice site)
680680CONFLICTL -> F (in Ref. 1; AAC35000).might get lost (downstream of altered splice site)
702702CONFLICTN -> S (in Ref. 1; AAC35000).might get lost (downstream of altered splice site)
707707ACT_SITEProton donor (By similarity).might get lost (downstream of altered splice site)
757757BINDINGNADP (By similarity).might get lost (downstream of altered splice site)
804806NP_BINDNADP (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 2739 / 2739
position (AA) of stopcodon in wt / mu AA sequence 913 / 913
position of stopcodon in wt / mu cDNA 2957 / 2957
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 219 / 219
chromosome 3
strand -1
last intron/exon boundary 2902
theoretical NMD boundary in CDS 2633
length of CDS 2739
coding sequence (CDS) position 1018
cDNA position
(for ins/del: last normal base / first normal base)		 1236
gDNA position
(for ins/del: last normal base / first normal base)		 51072
chromosomal position
(for ins/del: last normal base / first normal base)		 125865766
original gDNA sequence snippet CAGGTCTTGCTTTGCAGAGTGTTTGGCAGCGGATCCTCCCC
altered gDNA sequence snippet CAGGTCTTGCTTTGCAGAGTTTTTGGCAGCGGATCCTCCCC
original cDNA sequence snippet CTGCGGAGGCTGTGCGGAGTGTTTGGCAGCGGATCCTCCCC
altered cDNA sequence snippet CTGCGGAGGCTGTGCGGAGTTTTTGGCAGCGGATCCTCCCC
wildtype AA sequence MAGPSNPPAT MKIAVIGQSL FGQEVYCHLR KEGHEVVGVF TVPDKDGKAD PLGLEAEKDG
VPVFKYSRWR AKGQALPDVV AKYQALGAEL NVLPFCSQFI PMEIISAPRH GSIIYHPSLL
PRHRGASAIN WTLIHGDKKG GFSIFWADDG LDTGDLLLQK ECEVLPDDTV STLYNRFLFP
EGIKGMVQAV RLIAEGKAPR LPQPEEGATY EGIQKKETAK INWDQPAEAI HNWIRGNDKV
PGAWTEACEQ KLTFFNSTLN TSGLVPEGDA LPIPGAHRPG VVTKAGLILF GNDDKMLLVK
NIQLEDGKMI LASNFFKGAA SSVLELTEAE LVTAEAVRSV WQRILPKVLE VEDSTDFFKS
GAASVDVVRL VEEVKELCDG LELENEDVYM ASTFGDFIQL LVRKLRGDDE EGECSIDYVE
MAVNKRTVRM PHQLFIGGEF VDAEGAKTSE TINPTDGSVI CQVSLAQVTD VDKAVAAAKD
AFENGRWGKI SARDRGRLMY RLADLMEQHQ EELATIEALD AGAVYTLALK THVGMSIQTF
RYFAGWCDKI QGSTIPINQA RPNRNLTLTR KEPVGVCGII IPWNYPLMML SWKTAACLAA
GNTVVIKPAQ VTPLTALKFA ELTLKAGIPK GVVNVLPGSG SLVGQRLSDH PDVRKIGFTG
STEVGKHIMK SCAISNVKKV SLELGGKSPL IIFADCDLNK AVQMGMSSVF FNKGENCIAA
GRLFVEDSIH DEFVRRVVEE VRKMKVGNPL DRDTDHGPQN HHAHLVKLME YCQHGVKEGA
TLVCGGNQVP RPGFFFEPTV FTDVEDHMFI AKEESFGPVM IISRFADGDL DAVLSRANAT
EFGLASGVFT RDINKALYVS DKLQAGTVFV NTYNKTDVAA PFGGFKQSGF GKDLGEAALN
EYLRVKTVTF EY*
mutated AA sequence MAGPSNPPAT MKIAVIGQSL FGQEVYCHLR KEGHEVVGVF TVPDKDGKAD PLGLEAEKDG
VPVFKYSRWR AKGQALPDVV AKYQALGAEL NVLPFCSQFI PMEIISAPRH GSIIYHPSLL
PRHRGASAIN WTLIHGDKKG GFSIFWADDG LDTGDLLLQK ECEVLPDDTV STLYNRFLFP
EGIKGMVQAV RLIAEGKAPR LPQPEEGATY EGIQKKETAK INWDQPAEAI HNWIRGNDKV
PGAWTEACEQ KLTFFNSTLN TSGLVPEGDA LPIPGAHRPG VVTKAGLILF GNDDKMLLVK
NIQLEDGKMI LASNFFKGAA SSVLELTEAE LVTAEAVRSF WQRILPKVLE VEDSTDFFKS
GAASVDVVRL VEEVKELCDG LELENEDVYM ASTFGDFIQL LVRKLRGDDE EGECSIDYVE
MAVNKRTVRM PHQLFIGGEF VDAEGAKTSE TINPTDGSVI CQVSLAQVTD VDKAVAAAKD
AFENGRWGKI SARDRGRLMY RLADLMEQHQ EELATIEALD AGAVYTLALK THVGMSIQTF
RYFAGWCDKI QGSTIPINQA RPNRNLTLTR KEPVGVCGII IPWNYPLMML SWKTAACLAA
GNTVVIKPAQ VTPLTALKFA ELTLKAGIPK GVVNVLPGSG SLVGQRLSDH PDVRKIGFTG
STEVGKHIMK SCAISNVKKV SLELGGKSPL IIFADCDLNK AVQMGMSSVF FNKGENCIAA
GRLFVEDSIH DEFVRRVVEE VRKMKVGNPL DRDTDHGPQN HHAHLVKLME YCQHGVKEGA
TLVCGGNQVP RPGFFFEPTV FTDVEDHMFI AKEESFGPVM IISRFADGDL DAVLSRANAT
EFGLASGVFT RDINKALYVS DKLQAGTVFV NTYNKTDVAA PFGGFKQSGF GKDLGEAALN
EYLRVKTVTF EY*
speed 0.95 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