Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.836512127674614 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM086756)
  • known disease mutation: rs5047 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:53701879G>AN/A show variant in all transcripts   IGV
HGNC symbol AAAS
Ensembl transcript ID ENST00000394384
Genbank transcript ID NM_001173466
UniProt peptide Q9NRG9
alteration type single base exchange
alteration region CDS
DNA changes c.1189C>T
cDNA.1320C>T
g.16770C>T
AA changes L397F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 397
frameshift no
known variant Reference ID: rs121918551
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs5047 (pathogenic for Glucocorticoid deficiency with achalasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM086756)

known disease mutation at this position, please check HGMD for details (HGMD ID CM086756)
known disease mutation at this position, please check HGMD for details (HGMD ID CM086756)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.491
2.9361
(flanking)0.1630.998
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 increased16776wt: 0.9451 / mu: 0.9729 (marginal change - not scored)wt: AACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTGTG
mu: AACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTGTG		 tttc|GCAC
Acc marginally increased16780wt: 0.9236 / mu: 0.9753 (marginal change - not scored)wt: AGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTGTGTTTG
mu: AGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTGTGTTTG		 gcac|TCGA
Acc increased16774wt: 0.42 / mu: 0.50wt: TAAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTG
mu: TAAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTG		 tttt|TCGC
Acc increased16773wt: 0.55 / mu: 0.73wt: GTAAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCT
mu: GTAAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCT		 cttt|TTCG
Acc marginally increased16777wt: 0.9526 / mu: 0.9560 (marginal change - not scored)wt: ACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTGTGT
mu: ACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTGTGT		 ttcg|CACT
Acc marginally increased16778wt: 0.9710 / mu: 0.9866 (marginal change - not scored)wt: CCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTGTGTT
mu: CCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTGTGTT		 tcgc|ACTC
Acc increased16772wt: 0.38 / mu: 0.46wt: GGTAAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCC
mu: GGTAAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCC		 cctt|TTTC
Acc increased16775wt: 0.68 / mu: 0.80wt: AAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGCCCTGT
mu: AAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGCCCTGT		 tttt|CGCA
distance from splice site 39
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      397PRVQDGKPVILLFRTRNSPVFELL
mutated  not conserved    397PRVQDGKPVILFFRTRNSPVFEL
Ptroglodytes  all identical  ENSPTRG00000005012  430VQDGKPVILLFRTRNSPVFEL
Mmulatta  no alignment  ENSMMUG00000022036  n/a
Fcatus  all identical  ENSFCAG00000005881  430VQDGKPVILLFRTRNSPVFEL
Mmusculus  all identical  ENSMUSG00000036678  430VQDGNPVILLFRTRNSPVFEL
Ggallus  all conserved  ENSGALG00000013597  281PRTAGTQTVVAVFRTRNSPVFEL
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000019547  413QSTDHPSVIAVFKTRCSPAFEL
Dmelanogaster  not conserved  FBgn0030122  414NCIAVFRTFIQKFDLQISAAYYL
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000012664  436PEFEESQPVIAVFRTRNSPIFEL
protein features
start (aa)end (aa)featuredetails 
479479CONFLICTI -> V (in Ref. 5; BAA91394).might get lost (downstream of altered splice site)
495495MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
544546MOTIFMicrobody targeting signal (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1542 / 1542
position (AA) of stopcodon in wt / mu AA sequence 514 / 514
position of stopcodon in wt / mu cDNA 1673 / 1673
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 132 / 132
chromosome 12
strand -1
last intron/exon boundary 1449
theoretical NMD boundary in CDS 1267
length of CDS 1542
coding sequence (CDS) position 1189
cDNA position
(for ins/del: last normal base / first normal base)		 1320
gDNA position
(for ins/del: last normal base / first normal base)		 16770
chromosomal position
(for ins/del: last normal base / first normal base)		 53701879
original gDNA sequence snippet ATGGTAAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGC
altered gDNA sequence snippet ATGGTAAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGC
original cDNA sequence snippet ATGGTAAACCAGTCATCCTCCTTTTTCGCACTCGAAACAGC
altered cDNA sequence snippet ATGGTAAACCAGTCATCCTCTTTTTTCGCACTCGAAACAGC
wildtype AA sequence MCSLGLFPPP PPRGQVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNCT IVPSLKHRLQ RNVASLAWKP LSASVLAVAC
QSCILIWTLD PTSLSTRPSS GCAQVLSHPG HTPVTSLAWA PSGGRLLSAS PVDAAIRVWD
VSTETCVPLP WFRGGGVTNL LWSPDGSKIL ATTPSAVFRV WEAQMWTCER WPTLSGRCQT
GCWSPDGSRL LFTVLGEPLI YSLSFPERCG EGKGCVGGAK SATIVADLSE TTIQTPDGEE
RLGGEAHSMV WDPSGERLAV LMKGKPRVQD GKPVILLFRT RNSPVFELLP CGIIQGEPGA
QPQLITFHPS FNKGALLSVG WSTGRIAHIP LYFVNAQFPR FSPVLGRAQE PPAGGGGSIH
DLPLFTETSP TSAPWDPLPG PPPVLPHSPH SHL*
mutated AA sequence MCSLGLFPPP PPRGQVTLYE HNNELVTGSS YESPPPDFRG QWINLPVLQL TKDPLKTPGR
LDHGTRTAFI HHREQVWKRC INIWRDVGLF GVLNEIANSE EEVFEWVKTA SGWALALCRW
ASSLHGSLFP HLSLRSEDLI AEFAQVTNCT IVPSLKHRLQ RNVASLAWKP LSASVLAVAC
QSCILIWTLD PTSLSTRPSS GCAQVLSHPG HTPVTSLAWA PSGGRLLSAS PVDAAIRVWD
VSTETCVPLP WFRGGGVTNL LWSPDGSKIL ATTPSAVFRV WEAQMWTCER WPTLSGRCQT
GCWSPDGSRL LFTVLGEPLI YSLSFPERCG EGKGCVGGAK SATIVADLSE TTIQTPDGEE
RLGGEAHSMV WDPSGERLAV LMKGKPRVQD GKPVILFFRT RNSPVFELLP CGIIQGEPGA
QPQLITFHPS FNKGALLSVG WSTGRIAHIP LYFVNAQFPR FSPVLGRAQE PPAGGGGSIH
DLPLFTETSP TSAPWDPLPG PPPVLPHSPH SHL*
speed 0.81 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