Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999958 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002057)
  • known disease mutation: rs6617 (pathogenic)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:74531952C>TN/A show variant in all transcripts   IGV
HGNC symbol ALDH6A1
Ensembl transcript ID ENST00000553458
Genbank transcript ID NM_005589
UniProt peptide Q02252
alteration type single base exchange
alteration region CDS
DNA changes c.1336G>A
cDNA.1435G>A
g.19245G>A
AA changes G446R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 446
frameshift no
known variant Reference ID: rs72552258
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs6617 (pathogenic for Methylmalonate semialdehyde dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002057)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.2891
6.2891
(flanking)0.7131
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 increased19250wt: 0.3247 / mu: 0.3554 (marginal change - not scored)wt: GGAACTGCCATCTTC
mu: AGAACTGCCATCTTC		 AACT|gcca
Donor increased19237wt: 0.43 / mu: 0.63wt: CCCATATGGAAATGG
mu: CCCATATGGAAATAG		 CATA|tgga
Donor increased19243wt: 0.49 / mu: 0.74wt: TGGAAATGGAACTGC
mu: TGGAAATAGAACTGC		 GAAA|tgga
distance from splice site 69
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      446IQIVNNNPYGNGTAIFTTNGATAR
mutated  not conserved    446IQIVNNNPYGNRTAIFTTNGATA
Ptroglodytes  all identical  ENSPTRG00000006531  405IQIVNNNPYGNGTAIFTTNGATA
Mmulatta  all identical  ENSMMUG00000012684  450IQIVNNNPYGNGTAIFTTNGATA
Fcatus  all identical  ENSFCAG00000006202  447IKIVNDNPYGNGTAIFTTNGATA
Mmusculus  all identical  ENSMUSG00000021238  446IKIVNDNPYGNGTAIFTTNGATA
Ggallus  all identical  ENSGALG00000010211  449IEVVNNNPYGNGTAIFTTNGATA
Trubripes  all identical  ENSTRUG00000018226  436ICMVNRNPYGNGTAIFTT
Drerio  all identical  ENSDARG00000053485  436IKIVNKNPYGNGTAIFTTNGAAA
Dmelanogaster  all identical  FBgn0023537  432IGIVNANPYGNGTAVFT
Celegans  all identical  F13D12.4  436IEIINNNPYGNGTAIFTSNGATA
Xtropicalis  all identical  ENSXETG00000013304  434LKIVNSNPYGNGTAIFT
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1608 / 1608
position (AA) of stopcodon in wt / mu AA sequence 536 / 536
position of stopcodon in wt / mu cDNA 1707 / 1707
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 100 / 100
chromosome 14
strand -1
last intron/exon boundary 1603
theoretical NMD boundary in CDS 1453
length of CDS 1608
coding sequence (CDS) position 1336
cDNA position
(for ins/del: last normal base / first normal base)		 1435
gDNA position
(for ins/del: last normal base / first normal base)		 19245
chromosomal position
(for ins/del: last normal base / first normal base)		 74531952
original gDNA sequence snippet ATAACAACCCATATGGAAATGGAACTGCCATCTTCACCACC
altered gDNA sequence snippet ATAACAACCCATATGGAAATAGAACTGCCATCTTCACCACC
original cDNA sequence snippet ATAACAACCCATATGGAAATGGAACTGCCATCTTCACCACC
altered cDNA sequence snippet ATAACAACCCATATGGAAATAGAACTGCCATCTTCACCACC
wildtype AA sequence MAALLAAAAV RARILQVSSK VKSSPTWYSA SSFSSSVPTV KLFIGGKFVE SKSDKWIDIH
NPATNEVIGR VPQATKAEMD AAIASCKRAF PAWADTSVLS RQQVLLRYQQ LIKENLKEIA
KLITLEQGKT LADAEGDVFR GLQVVEHACS VTSLMMGETM PSITKDMDLY SYRLPLGVCA
GIAPFNFPAM IPLWMFPMAM VCGNTFLMKP SERVPGATML LAKLLQDSGA PDGTLNIIHG
QHEAVNFICD HPDIKAISFV GSNKAGEYIF ERGSRHGKRV QANMGAKNHG VVMPDANKEN
TLNQLVGAAF GAAGQRCMAL STAVLVGEAK KWLPELVEHA KNLRVNAGDQ PGADLGPLIT
PQAKERVCNL IDSGTKEGAS ILLDGRKIKV KGYENGNFVG PTIISNVKPN MTCYKEEIFG
PVLVVLETET LDEAIQIVNN NPYGNGTAIF TTNGATARKY AHLVDVGQVG VNVPIPVPLP
MFSFTGSRSS FRGDTNFYGK QGIQFYTQLK TITSQWKEED ATLSSPAVVM PTMGR*
mutated AA sequence MAALLAAAAV RARILQVSSK VKSSPTWYSA SSFSSSVPTV KLFIGGKFVE SKSDKWIDIH
NPATNEVIGR VPQATKAEMD AAIASCKRAF PAWADTSVLS RQQVLLRYQQ LIKENLKEIA
KLITLEQGKT LADAEGDVFR GLQVVEHACS VTSLMMGETM PSITKDMDLY SYRLPLGVCA
GIAPFNFPAM IPLWMFPMAM VCGNTFLMKP SERVPGATML LAKLLQDSGA PDGTLNIIHG
QHEAVNFICD HPDIKAISFV GSNKAGEYIF ERGSRHGKRV QANMGAKNHG VVMPDANKEN
TLNQLVGAAF GAAGQRCMAL STAVLVGEAK KWLPELVEHA KNLRVNAGDQ PGADLGPLIT
PQAKERVCNL IDSGTKEGAS ILLDGRKIKV KGYENGNFVG PTIISNVKPN MTCYKEEIFG
PVLVVLETET LDEAIQIVNN NPYGNRTAIF TTNGATARKY AHLVDVGQVG VNVPIPVPLP
MFSFTGSRSS FRGDTNFYGK QGIQFYTQLK TITSQWKEED ATLSSPAVVM PTMGR*
speed 1.06 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