Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999990404836196 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM080148)
  • known disease mutation: rs18369 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233393011T>CN/A show variant in all transcripts   IGV
HGNC symbol CHRND
Ensembl transcript ID ENST00000536614
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region CDS
DNA changes c.283T>C
cDNA.311T>C
g.2309T>C
AA changes F95L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 95
frameshift no
known variant Reference ID: rs121909506
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18369 (pathogenic for Lethal multiple pterygium syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)

known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)
known disease mutation at this position, please check HGMD for details (HGMD ID CM080148)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9620.078
4.2610.996
(flanking)2.5691
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2311wt: 0.30 / mu: 0.45wt: GAATTTGGAAACATC
mu: GAACTTGGAAACATC		 ATTT|ggaa
Donor marginally increased2300wt: 0.8294 / mu: 0.8926 (marginal change - not scored)wt: GGAATGCTGAAGAAT
mu: GGAATGCTGAAGAAC		 AATG|ctga
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      95TDNRLKWNAEEFGNISVLRLPPDM
mutated  not conserved    95TDNRLKWNAEELGNISVLRLPPD
Ptroglodytes  all identical  ENSPTRG00000013040  95TDNRLKWNAEEFGNISVLRLPPD
Mmulatta  all identical  ENSMMUG00000022147  95TDNRLKWNAEEFGNISVLRLPPD
Fcatus  all identical  ENSFCAG00000005679  94TDPRLQWDAEEFGNISVLRLPP-
Mmusculus  all identical  ENSMUSG00000026251  98VDSRLQWDANDFGNITVLRLPPD
Ggallus  all identical  ENSGALG00000007899  92TDYRLQWNTSEFGGVDVLRLLPE
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000019342  95KDHRLTWNESEY-DIPVLRLPPS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000027884  95YDKRLAWDMEEFHHINIIRVPPD
protein features
start (aa)end (aa)featuredetails 
22245TOPO_DOMExtracellular (Potential).lost
9797CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
151151DISULFIDBy similarity.might get lost (downstream of altered splice site)
164164CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
165165DISULFIDBy similarity.might get lost (downstream of altered splice site)
246270TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
278299TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
312333TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
334471TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
390390MOD_RESPhosphotyrosine; by Tyr-kinases (By similarity).might get lost (downstream of altered splice site)
472490TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 708 / 708
position (AA) of stopcodon in wt / mu AA sequence 236 / 236
position of stopcodon in wt / mu cDNA 736 / 736
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 29 / 29
chromosome 2
strand 1
last intron/exon boundary 851
theoretical NMD boundary in CDS 772
length of CDS 708
coding sequence (CDS) position 283
cDNA position
(for ins/del: last normal base / first normal base)		 311
gDNA position
(for ins/del: last normal base / first normal base)		 2309
chromosomal position
(for ins/del: last normal base / first normal base)		 233393011
original gDNA sequence snippet TGAAGTGGAATGCTGAAGAATTTGGAAACATCAGTGTCCTG
altered gDNA sequence snippet TGAAGTGGAATGCTGAAGAACTTGGAAACATCAGTGTCCTG
original cDNA sequence snippet TGAAGTGGAATGCTGAAGAATTTGGAAACATCAGTGTCCTG
altered cDNA sequence snippet TGAAGTGGAATGCTGAAGAACTTGGAAACATCAGTGTCCTG
wildtype AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLKEVE ETLTTNVWIE HGWTDNRLKW NAEEFGNISV LRLPPDMVWL PEIVLENNND
GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFR ERGVGDSPPA
GQGQRGPQSP SGQPQPPGHH LLPHHPPQAP LLHHQHPGAL RAHLLHGQPG LLPTG*
mutated AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLKEVE ETLTTNVWIE HGWTDNRLKW NAEELGNISV LRLPPDMVWL PEIVLENNND
GSFQISYSCN VLVYHYGFVY WLPPAIFRSS CPISVTYFPF DWQNCSLKFR ERGVGDSPPA
GQGQRGPQSP SGQPQPPGHH LLPHHPPQAP LLHHQHPGAL RAHLLHGQPG LLPTG*
speed 0.96 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