Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999980294958 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030015)
  • known disease mutation: rs18364 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:233394841C>AN/A show variant in all transcripts   IGV
HGNC symbol CHRND
Ensembl transcript ID ENST00000543200
Genbank transcript ID N/A
UniProt peptide Q07001
alteration type single base exchange
alteration region CDS
DNA changes c.767C>A
cDNA.823C>A
g.4139C>A
AA changes P256Q Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 256
frameshift no
known variant Reference ID: rs121909503
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs18364 (pathogenic for Congenital myasthenic syndrome 3B) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030015)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.021
4.360.999
(flanking)-2.4090.009
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 increased4139wt: 0.3633 / mu: 0.3942 (marginal change - not scored)wt: CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG
mu: CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG		 tacc|GGCT
Acc gained41380.33mu: TCAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCA ctac|AGGC
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      256ISFMVNLVFYLPADSGEKTSVAIS
mutated  not conserved    256ISFMVNLVFYLQADSGEKTSVAI
Ptroglodytes  all identical  ENSPTRG00000013040  271ISFMVNLVFYLPADSGEKTSVAI
Mmulatta  all identical  ENSMMUG00000022147  271ISFMVNLVFYLPADSGEKTSVAI
Fcatus  all identical  ENSFCAG00000005679  267ISFMINLVFYLPADSGEKTSMAI
Mmusculus  all identical  ENSMUSG00000026251  274ISFMINLVFYLPGDCGEKTSVAI
Ggallus  all identical  ENSGALG00000007899  270IAFMAILVFYLPADSGEKMTLVI
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000019342  270SFLASLVYYLPADSGEKMTLSI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000027884  273IALMANLVFYLPADSGEKMTLAI
protein features
start (aa)end (aa)featuredetails 
246270TRANSMEMHelical; (Potential).lost
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 1509 / 1509
position (AA) of stopcodon in wt / mu AA sequence 503 / 503
position of stopcodon in wt / mu cDNA 1565 / 1565
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 57 / 57
chromosome 2
strand 1
last intron/exon boundary 1383
theoretical NMD boundary in CDS 1276
length of CDS 1509
coding sequence (CDS) position 767
cDNA position
(for ins/del: last normal base / first normal base)		 823
gDNA position
(for ins/del: last normal base / first normal base)		 4139
chromosomal position
(for ins/del: last normal base / first normal base)		 233394841
original gDNA sequence snippet CAACCTGGTCTTCTACCTACCGGCTGACAGTGAGCCTCCAG
altered gDNA sequence snippet CAACCTGGTCTTCTACCTACAGGCTGACAGTGAGCCTCCAG
original cDNA sequence snippet CAACCTGGTCTTCTACCTACCGGCTGACAGTGGTGAGAAGA
altered cDNA sequence snippet CAACCTGGTCTTCTACCTACAGGCTGACAGTGGTGAGAAGA
wildtype AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLGWTD NRLKWNAEEF GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLPADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*
mutated AA sequence MEGPVLTLGL LAALAVCGSW GLNEEERLIR HLFQEKGYNK ELRPVAHKEE SVDVALALTL
SNLISLGWTD NRLKWNAEEF GNISVLRLPP DMVWLPEIVL ENNNDGSFQI SYSCNVLVYH
YGFVYWLPPA IFRSSCPISV TYFPFDWQNC SLKFSSLKYT AKEITLSLKQ DAKENRTYPV
EWIIIDPEGF TENGEWEIVH RPARVNVDPR APLDSPSRQD ITFYLIIRRK PLFYIINILV
PCVLISFMVN LVFYLQADSG EKTSVAISVL LAQSVFLLLI SKRLPATSMA IPLIGKFLLF
GMVLVTMVVV ICVIVLNIHF RTPSTHVLSE GVKKLFLETL PELLHMSRPA EDGPSPGALV
RRSSSLGYIS KAEEYFLLKS RSDLMFEKQS ERHGLARRLT TARRPPASSE QAQQELFNEL
KPAVDGANFI VNHMRDQNNY NEEKDSWNRV ARTVDRLCLF VVTPVMVVGT AWIFLQGVYN
QPPPQPFPGD PYSYNVQDKR FI*
speed 1.26 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