Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.0705178662915554 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM072835)
  • known disease mutation: rs18113 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:52021009C>TN/A show variant in all transcripts   IGV
HGNC symbol ACY1
Ensembl transcript ID ENST00000476351
Genbank transcript ID NM_001198898
UniProt peptide Q03154
alteration type single base exchange
alteration region CDS
DNA changes c.484C>T
cDNA.649C>T
g.11944C>T
AA changes R162W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 162
frameshift no
known variant Reference ID: rs121912700
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18113 (pathogenic for Aminoacylase 1 deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM072835)

known disease mutation at this position, please check HGMD for details (HGMD ID CM072835)
known disease mutation at this position, please check HGMD for details (HGMD ID CM072835)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0260.688
1.7470.679
(flanking)0.8880.476
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 increased11935wt: 0.6770 / mu: 0.7186 (marginal change - not scored)wt: TGCCTTCCCCCTACACCTCCCCAGGGGTGCGGGTTACCAGC
mu: TGCCTTCCCCCTACACCTCCCCAGGGGTGTGGGTTACCAGC		 tccc|CAGG
Acc marginally decreased11938wt: 0.9542 / mu: 0.9480 (marginal change - not scored)wt: CTTCCCCCTACACCTCCCCAGGGGTGCGGGTTACCAGCACT
mu: CTTCCCCCTACACCTCCCCAGGGGTGTGGGTTACCAGCACT		 ccag|GGGT
Donor marginally increased11937wt: 0.8749 / mu: 0.9227 (marginal change - not scored)wt: TCCCCAGGGGTGCGG
mu: TCCCCAGGGGTGTGG		 CCCA|gggg
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      162VFYSERSPWWVRVTSTGRPGHASR
mutated  not conserved    162VFYSERSPWWVWVTSTGRPGHAS
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000003646  60VFYSERSPWWVRVTSTGRPGHGS
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000023262  197VFYSERSPWWVQVTSTGKPGHAS
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000014223  208FYGERNPWWITIHCPGSPGHGS
Drerio  not conserved  ENSDARG00000038475  209VFYGERNPWWITVRCPGSPGHGS
Dmelanogaster  all identical  FBgn0039049  197YYAERTLWHLRFKISGTAGHGS
Celegans  all conserved  C06A6.4  192YAERIPWWVKVTLPGHPGHGS
Xtropicalis  not conserved  ENSXETG00000000089  209VFYGEKCPWWITVHCGGDPGHGS
protein features
start (aa)end (aa)featuredetails 
162165HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1122 / 1122
position (AA) of stopcodon in wt / mu AA sequence 374 / 374
position of stopcodon in wt / mu cDNA 1287 / 1287
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 166 / 166
chromosome 3
strand 1
last intron/exon boundary 1123
theoretical NMD boundary in CDS 907
length of CDS 1122
coding sequence (CDS) position 484
cDNA position
(for ins/del: last normal base / first normal base)		 649
gDNA position
(for ins/del: last normal base / first normal base)		 11944
chromosomal position
(for ins/del: last normal base / first normal base)		 52021009
original gDNA sequence snippet CCTACACCTCCCCAGGGGTGCGGGTTACCAGCACTGGGAGG
altered gDNA sequence snippet CCTACACCTCCCCAGGGGTGTGGGTTACCAGCACTGGGAGG
original cDNA sequence snippet AGCGGAGTCCCTGGTGGGTGCGGGTTACCAGCACTGGGAGG
altered cDNA sequence snippet AGCGGAGTCCCTGGTGGGTGTGGGTTACCAGCACTGGGAGG
wildtype AA sequence MTSKGPEEEH PSVTLFRQYL RIRTVQPKPD YGTNPTLSSI LLNSHTDVVP VFKEHWSHDP
FEAFKDSEGY IYARGAQDMK CVSIQYLEAV RRLKVEGHRF PRTIHMTFVP DEEVGGHQGM
ELFVQRPEFH ALRAGFALDE GIANPTDAFT VFYSERSPWW VRVTSTGRPG HASRFMEDTA
AEKLHKVVNS ILAFREKEWQ RLQSNPHLKE GSVTSVNLTK LEGGVAYNVI PATMSASFDF
RVAPDVDFKA FEEQLQSWCQ AAGEGVTLEF AQKWMHPQVT PTDDSNPWWA AFSRVCKDMN
LTLEPEIMPA ATDNRYIRAV GVPALGFSPM NRTPVLLHDH DERLHEAVFL RGVDIYTRLL
PALASVPALP SDS*
mutated AA sequence MTSKGPEEEH PSVTLFRQYL RIRTVQPKPD YGTNPTLSSI LLNSHTDVVP VFKEHWSHDP
FEAFKDSEGY IYARGAQDMK CVSIQYLEAV RRLKVEGHRF PRTIHMTFVP DEEVGGHQGM
ELFVQRPEFH ALRAGFALDE GIANPTDAFT VFYSERSPWW VWVTSTGRPG HASRFMEDTA
AEKLHKVVNS ILAFREKEWQ RLQSNPHLKE GSVTSVNLTK LEGGVAYNVI PATMSASFDF
RVAPDVDFKA FEEQLQSWCQ AAGEGVTLEF AQKWMHPQVT PTDDSNPWWA AFSRVCKDMN
LTLEPEIMPA ATDNRYIRAV GVPALGFSPM NRTPVLLHDH DERLHEAVFL RGVDIYTRLL
PALASVPALP SDS*
speed 0.98 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