Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995608 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012724)
  • known disease mutation: rs1359 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:24528277G>AN/A show variant in all transcripts   IGV
HGNC symbol ALDH5A1
Ensembl transcript ID ENST00000357578
Genbank transcript ID NM_001080
UniProt peptide P51649
alteration type single base exchange
alteration region CDS
DNA changes c.1226G>A
cDNA.1371G>A
g.33198G>A
AA changes G409D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 409
frameshift no
known variant Reference ID: rs118203984
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs1359 (pathogenic for Succinate-semialdehyde dehydrogenase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012724)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012724)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012724)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.8071
5.8071
(flanking)-0.6230.774
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased33199wt: 0.34 / mu: 0.81wt: ACAGGTGGAAAACGA
mu: ACAGATGGAAAACGA		 AGGT|ggaa
Donor increased33200wt: 0.49 / mu: 0.91wt: CAGGTGGAAAACGAC
mu: CAGATGGAAAACGAC		 GGTG|gaaa
Donor gained331940.59mu: TTGTGACAGATGGAA GTGA|caga
distance from splice site 53
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      409DAVSKGATVVTGGKRHQLGKNFFE
mutated  not conserved    409DAVSKGATVVTDGKRHQLGKNFF
Ptroglodytes  all identical  ENSPTRG00000017776  409DAVSKGATVVTGGKRHQLGKNFF
Mmulatta  all identical  ENSMMUG00000019368  422TGGKRHHLGKNFF
Fcatus  all identical  ENSFCAG00000011094  304VVTGGKRHQLGKNFF
Mmusculus  all identical  ENSMUSG00000035936  397DAVAKGATVVTGGKRHQSGGNFF
Ggallus  all identical  ENSGALG00000012663  390DAVSQGASVVTGGKRHSLGKNFF
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000076544  389DAVDHGAVVVRGGKR-
Dmelanogaster  all identical  FBgn0039349  379NIILGGQPLPDKGSLFY
Celegans  all identical  F45H10.1  369DALGKGSELICGGKRGEHGTS-
Xtropicalis  all identical  ENSXETG00000021961  362NAVSLGAQIEAGGKRSAVGKNFF
protein features
start (aa)end (aa)featuredetails 
405408STRANDmight get lost (downstream of altered splice site)
423428STRANDmight get lost (downstream of altered splice site)
430433HELIXmight get lost (downstream of altered splice site)
441450STRANDmight get lost (downstream of altered splice site)
452459HELIXmight get lost (downstream of altered splice site)
466471STRANDmight get lost (downstream of altered splice site)
475484HELIXmight get lost (downstream of altered splice site)
487493STRANDmight get lost (downstream of altered splice site)
498498BINDINGSubstrate.might get lost (downstream of altered splice site)
498498MUTAGENS->A: Reduces catalytic activity to less than 15% of wild-type.might get lost (downstream of altered splice site)
508510HELIXmight get lost (downstream of altered splice site)
511513STRANDmight get lost (downstream of altered splice site)
517519TURNmight get lost (downstream of altered splice site)
520524HELIXmight get lost (downstream of altered splice site)
525532STRANDmight get lost (downstream of altered splice site)
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 1753 / 1753
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 146 / 146
chromosome 6
strand 1
last intron/exon boundary 1548
theoretical NMD boundary in CDS 1352
length of CDS 1608
coding sequence (CDS) position 1226
cDNA position
(for ins/del: last normal base / first normal base)		 1371
gDNA position
(for ins/del: last normal base / first normal base)		 33198
chromosomal position
(for ins/del: last normal base / first normal base)		 24528277
original gDNA sequence snippet AGGTGCCACCGTTGTGACAGGTGGAAAACGACACCAACTTG
altered gDNA sequence snippet AGGTGCCACCGTTGTGACAGATGGAAAACGACACCAACTTG
original cDNA sequence snippet AGGTGCCACCGTTGTGACAGGTGGAAAACGACACCAACTTG
altered cDNA sequence snippet AGGTGCCACCGTTGTGACAGATGGAAAACGACACCAACTTG
wildtype AA sequence MATCIWLRSC GARRLGSTFP GCRLRPRAGG LVPASGPAPG PAQLRCYAGR LAGLSAALLR
TDSFVGGRWL PAAATFPVQD PASGAALGMV ADCGVREARA AVRAAYEAFC RWREVSAKER
SSLLRKWYNL MIQNKDDLAR IITAESGKPL KEAHGEILYS AFFLEWFSEE ARRVYGDIIH
TPAKDRRALV LKQPIGVAAV ITPWNFPSAM ITRKVGAALA AGCTVVVKPA EDTPFSALAL
AELASQAGIP SGVYNVIPCS RKNAKEVGEA ICTDPLVSKI SFTGSTTTGK ILLHHAANSV
KRVSMELGGL APFIVFDSAN VDQAVAGAMA SKFRNTGQTC VCSNQFLVQR GIHDAFVKAF
AEAMKKNLRV GNGFEEGTTQ GPLINEKAVE KVEKQVNDAV SKGATVVTGG KRHQLGKNFF
EPTLLCNVTQ DMLCTHEETF GPLAPVIKFD TEEEAIAIAN AADVGLAGYF YSQDPAQIWR
VAEQLEVGMV GVNEGLISSV ECPFGGVKQS GLGREGSKYG IDEYLELKYV CYGGL*
mutated AA sequence MATCIWLRSC GARRLGSTFP GCRLRPRAGG LVPASGPAPG PAQLRCYAGR LAGLSAALLR
TDSFVGGRWL PAAATFPVQD PASGAALGMV ADCGVREARA AVRAAYEAFC RWREVSAKER
SSLLRKWYNL MIQNKDDLAR IITAESGKPL KEAHGEILYS AFFLEWFSEE ARRVYGDIIH
TPAKDRRALV LKQPIGVAAV ITPWNFPSAM ITRKVGAALA AGCTVVVKPA EDTPFSALAL
AELASQAGIP SGVYNVIPCS RKNAKEVGEA ICTDPLVSKI SFTGSTTTGK ILLHHAANSV
KRVSMELGGL APFIVFDSAN VDQAVAGAMA SKFRNTGQTC VCSNQFLVQR GIHDAFVKAF
AEAMKKNLRV GNGFEEGTTQ GPLINEKAVE KVEKQVNDAV SKGATVVTDG KRHQLGKNFF
EPTLLCNVTQ DMLCTHEETF GPLAPVIKFD TEEEAIAIAN AADVGLAGYF YSQDPAQIWR
VAEQLEVGMV GVNEGLISSV ECPFGGVKQS GLGREGSKYG IDEYLELKYV CYGGL*
speed 0.51 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