Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • 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 ENST00000457943
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region CDS
DNA changes c.12T>C
cDNA.311T>C
g.2309T>C
AA changes no AA changes
position(s) of altered AA
if AA alteration in CDS		 N/A
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		 N/A
protein features
start (aa)end (aa)featuredetails 
121SIGNALBy similarity.might get lost (downstream of altered splice site)
22245TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 no
position of stopcodon in wt / mu CDS 972 / 972
position (AA) of stopcodon in wt / mu AA sequence 324 / 324
position of stopcodon in wt / mu cDNA 1271 / 1271
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 300 / 300
chromosome 2
strand 1
last intron/exon boundary 1089
theoretical NMD boundary in CDS 739
length of CDS 972
coding sequence (CDS) position 12
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 MLKNLETSVS CASPRTWCGS QRLCWRTTMT APSRSPTPAT CLSTTTASCT GCHLPSSAPP
APSLSPISPS TGRTAPSSSG GEKTSVAISV LLAQSVFLLL ISKRLPATSM AIPLIGKFLL
FGMVLVTMVV VICVIVLNIH FRTPSTHVLS EGVKKLFLET LPELLHMSRP AEDGPSPGAL
VRRSSSLGYI SKAEEYFLLK SRSDLMFEKQ SERHGLARRL TTARRPPASS EQAQQELFNE
LKPAVDGANF IVNHMRDQNN YNEEKDSWNR VARTVDRLCL FVVTPVMVVG TAWIFLQGVY
NQPPPQPFPG DPYSYNVQDK RFI*
mutated AA sequence MLKNLETSVS CASPRTWCGS QRLCWRTTMT APSRSPTPAT CLSTTTASCT GCHLPSSAPP
APSLSPISPS TGRTAPSSSG GEKTSVAISV LLAQSVFLLL ISKRLPATSM AIPLIGKFLL
FGMVLVTMVV VICVIVLNIH FRTPSTHVLS EGVKKLFLET LPELLHMSRP AEDGPSPGAL
VRRSSSLGYI SKAEEYFLLK SRSDLMFEKQ SERHGLARRL TTARRPPASS EQAQQELFNE
LKPAVDGANF IVNHMRDQNN YNEEKDSWNR VARTVDRLCL FVVTPVMVVG TAWIFLQGVY
NQPPPQPFPG DPYSYNVQDK RFI*
speed 0.73 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