Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.876601728659361 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990501)
  • known disease mutation: rs9133 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21546501G>AN/A show variant in all transcripts   IGV
HGNC symbol ECE1
Ensembl transcript ID ENST00000357071
Genbank transcript ID NM_001113347
UniProt peptide P42892
alteration type single base exchange
alteration region CDS
DNA changes c.2224C>T
cDNA.2339C>T
g.125497C>T
AA changes R742C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 742
frameshift no
known variant Reference ID: rs3026906
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC02626

known disease mutation: rs9133 (pathogenic for Hirschsprung disease, cardiac defects, and autonomic dysfunction) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990501)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990501)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990501)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1580.959
1.8070.998
(flanking)1.3241
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 increased125508wt: 0.9681 / mu: 0.9766 (marginal change - not scored)wt: GAACACTTCCGCTGCCCACCTGGCTCACCCATGAACCCGCC
mu: GAACACTTCTGCTGCCCACCTGGCTCACCCATGAACCCGCC		 acct|GGCT
Acc increased125504wt: 0.41 / mu: 0.48wt: CTCAGAACACTTCCGCTGCCCACCTGGCTCACCCATGAACC
mu: CTCAGAACACTTCTGCTGCCCACCTGGCTCACCCATGAACC		 gccc|ACCT
distance from splice site 124
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      742LSNSKEFSEHFRCPPGSPMNPPHK
mutated  not conserved    742LSNSKEFSEHFCCPPGSPMNPPH
Ptroglodytes  not conserved  ENSPTRG00000000298  754LSNSKEFSEHFHCPLGSPM
Mmulatta  not conserved  ENSMMUG00000010942  751LSNSKEFSEHFHCSPGSPM
Fcatus  not conserved  ENSFCAG00000014530  736VSNSKEFSEHFHCPPGSPMNPHH
Mmusculus  all identical  ENSMUSG00000057530  737LSNSKEFSEHFRCPPGSPMNPHH
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000012021  754ISNSREFSEHFGCKADAPMNP
Drerio  not conserved  ENSDARG00000061737  781ISNSHEFSEHFGCKADSPMNPKR
Dmelanogaster  all conserved  FBgn0031081  770LSNMKEFAEVFQCKPGKRMNPTE
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023235  528VSNSQEFAEHFRCPPGSPMNPRN
protein features
start (aa)end (aa)featuredetails 
90770TOPO_DOMExtracellular (Potential).lost
735744HELIXlost
747753HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2277 / 2277
position (AA) of stopcodon in wt / mu AA sequence 759 / 759
position of stopcodon in wt / mu cDNA 2392 / 2392
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 116 / 116
chromosome 1
strand -1
last intron/exon boundary 2216
theoretical NMD boundary in CDS 2050
length of CDS 2277
coding sequence (CDS) position 2224
cDNA position
(for ins/del: last normal base / first normal base)		 2339
gDNA position
(for ins/del: last normal base / first normal base)		 125497
chromosomal position
(for ins/del: last normal base / first normal base)		 21546501
original gDNA sequence snippet AGGAGTTCTCAGAACACTTCCGCTGCCCACCTGGCTCACCC
altered gDNA sequence snippet AGGAGTTCTCAGAACACTTCTGCTGCCCACCTGGCTCACCC
original cDNA sequence snippet AGGAGTTCTCAGAACACTTCCGCTGCCCACCTGGCTCACCC
altered cDNA sequence snippet AGGAGTTCTCAGAACACTTCTGCTGCCCACCTGGCTCACCC
wildtype AA sequence MPLQGLGLQR NPFLQGKRGP GLTSSPPLLP PSLQVNFHSP RSGQRCWAAR TQVEKRLVVL
VVLLAAGLVA CLAALGIQYQ TRSPSVCLSE ACVSVTSSIL SSMDPTVDPC HDFFSYACGG
WIKANPVPDG HSRWGTFSNL WEHNQAIIKH LLENSTASVS EAERKAQVYY RACMNETRIE
ELRAKPLMEL IERLGGWNIT GPWAKDNFQD TLQVVTAHYR TSPFFSVYVS ADSKNSNSNV
IQVDQSGLGL PSRDYYLNKT ENEKVLTGYL NYMVQLGKLL GGGDEEAIRP QMQQILDFET
ALANITIPQE KRRDEELIYH KVTAAELQTL APAINWLPFL NTIFYPVEIN ESEPIVVYDK
EYLEQISTLI NTTDRCLLNN YMIWNLVRKT SSFLDQRFQD ADEKFMEVMY GTKKTCLPRW
KFCVSDTENN LGFALGPMFV KATFAEDSKS IATEIILEIK KAFEESLSTL KWMDEETRKS
AKEKADAIYN MIGYPNFIMD PKELDKVFND YTAVPDLYFE NAMRFFNFSW RVTADQLRKA
PNRDQWSMTP PMVNAYYSPT KNEIVFPAGI LQAPFYTRSS PKALNFGGIG VVVGHELTHA
FDDQGREYDK DGNLRPWWKN SSVEAFKRQT ECMVEQYSNY SVNGEPVNGR HTLGENIADN
GGLKAAYRAY QNWVKKNGAE HSLPTLGLTN NQLFFLGFAQ VWCSVRTPES SHEGLITDPH
SPSRFRVIGS LSNSKEFSEH FRCPPGSPMN PPHKCEVW*
mutated AA sequence MPLQGLGLQR NPFLQGKRGP GLTSSPPLLP PSLQVNFHSP RSGQRCWAAR TQVEKRLVVL
VVLLAAGLVA CLAALGIQYQ TRSPSVCLSE ACVSVTSSIL SSMDPTVDPC HDFFSYACGG
WIKANPVPDG HSRWGTFSNL WEHNQAIIKH LLENSTASVS EAERKAQVYY RACMNETRIE
ELRAKPLMEL IERLGGWNIT GPWAKDNFQD TLQVVTAHYR TSPFFSVYVS ADSKNSNSNV
IQVDQSGLGL PSRDYYLNKT ENEKVLTGYL NYMVQLGKLL GGGDEEAIRP QMQQILDFET
ALANITIPQE KRRDEELIYH KVTAAELQTL APAINWLPFL NTIFYPVEIN ESEPIVVYDK
EYLEQISTLI NTTDRCLLNN YMIWNLVRKT SSFLDQRFQD ADEKFMEVMY GTKKTCLPRW
KFCVSDTENN LGFALGPMFV KATFAEDSKS IATEIILEIK KAFEESLSTL KWMDEETRKS
AKEKADAIYN MIGYPNFIMD PKELDKVFND YTAVPDLYFE NAMRFFNFSW RVTADQLRKA
PNRDQWSMTP PMVNAYYSPT KNEIVFPAGI LQAPFYTRSS PKALNFGGIG VVVGHELTHA
FDDQGREYDK DGNLRPWWKN SSVEAFKRQT ECMVEQYSNY SVNGEPVNGR HTLGENIADN
GGLKAAYRAY QNWVKKNGAE HSLPTLGLTN NQLFFLGFAQ VWCSVRTPES SHEGLITDPH
SPSRFRVIGS LSNSKEFSEH FCCPPGSPMN PPHKCEVW*
speed 1.00 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