Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999998594976 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045935)
  • known disease mutation: rs11938 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:80878730C>TN/A show variant in all transcripts   IGV
HGNC symbol BCKDHB
Ensembl transcript ID ENST00000356489
Genbank transcript ID NM_000056
UniProt peptide P21953
alteration type single base exchange
alteration region CDS
DNA changes c.616C>T
cDNA.663C>T
g.62367C>T
AA changes H206Y Score: 83 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 206
frameshift no
known variant Reference ID: rs121965004
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs11938 (pathogenic for MAPLE SYRUP URINE DISEASE, CLASSIC, TYPE IB) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045935)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045935)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045935)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1730.998
5.41
(flanking)4.4681
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased62369wt: 0.25 / mu: 0.34wt: CCTGAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTATG
mu: CCTGAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTATG		 ccat|TGCC
Acc increased62370wt: 0.30 / mu: 0.40wt: CTGAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTATGT
mu: CTGAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTATGT		 catt|GCCC
Acc marginally increased62376wt: 0.8459 / mu: 0.8772 (marginal change - not scored)wt: CATTTTTTGCCCATTGCCCAGGAATCAAGGTATGTTCATTT
mu: CATTTTTTGCCTATTGCCCAGGAATCAAGGTATGTTCATTT		 ccag|GAAT
Acc marginally increased62367wt: 0.8622 / mu: 0.8646 (marginal change - not scored)wt: GTCCTGAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTA
mu: GTCCTGAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTA		 gccc|ATTG
Acc marginally increased62374wt: 0.4242 / mu: 0.4470 (marginal change - not scored)wt: AGCATTTTTTGCCCATTGCCCAGGAATCAAGGTATGTTCAT
mu: AGCATTTTTTGCCTATTGCCCAGGAATCAAGGTATGTTCAT		 gccc|AGGA
Acc increased62372wt: 0.43 / mu: 0.56wt: GAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTATGTTC
mu: GAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTATGTTC		 ttgc|CCAG
Donor increased62370wt: 0.43 / mu: 0.54wt: CCCATTGCCCAGGAA
mu: CCTATTGCCCAGGAA		 CATT|gccc
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      206YHSQSPEAFFAHCPGIKVVIPRSP
mutated  all conserved    206YHSQSPEAFFAYCPGIKVVIPRS
Ptroglodytes  all identical  ENSPTRG00000018372  206YHSQSPEAFFAHCPGIKVVIPRS
Mmulatta  not conserved  ENSMMUG00000004829  214FTKIVLKNLF-----LQVVIPRS
Fcatus  all identical  ENSFCAG00000010609  206YHSQSPEAFFAHCPGIKVVVPRS
Mmusculus  all identical  ENSMUSG00000032263  136YHSQSPEAFFAHCPGIKVVIPRS
Ggallus  all identical  ENSGALG00000015866  206YHSQSPEAFFAHCPGIKIVIPRS
Trubripes  all identical  ENSTRUG00000002294  206YHSQSPEAFFAHCPGIKVVIPRG
Drerio  no alignment  ENSDARG00000086611  n/a
Dmelanogaster  all identical  FBgn0039993  178YHSQSPEAYFAHTPGLRVVVPRG
Celegans  all identical  F27D4.5  180YHSQSPEANFTHTPGLKLVVPRG
Xtropicalis  all identical  ENSXETG00000011773  195YHSQSPEAFFAHAPGIKVVIPRS
protein features
start (aa)end (aa)featuredetails 
211213STRANDmight get lost (downstream of altered splice site)
218230HELIXmight get lost (downstream of altered splice site)
231233STRANDmight get lost (downstream of altered splice site)
235240STRANDmight get lost (downstream of altered splice site)
241241MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
241243HELIXmight get lost (downstream of altered splice site)
244246TURNmight get lost (downstream of altered splice site)
249254STRANDmight get lost (downstream of altered splice site)
264267STRANDmight get lost (downstream of altered splice site)
270276STRANDmight get lost (downstream of altered splice site)
280295HELIXmight get lost (downstream of altered splice site)
299303STRANDmight get lost (downstream of altered splice site)
306309STRANDmight get lost (downstream of altered splice site)
312322HELIXmight get lost (downstream of altered splice site)
322322CONFLICTT -> S (in Ref. 8; CAA36685).might get lost (downstream of altered splice site)
325333STRANDmight get lost (downstream of altered splice site)
337349HELIXmight get lost (downstream of altered splice site)
350352HELIXmight get lost (downstream of altered splice site)
358362STRANDmight get lost (downstream of altered splice site)
372375HELIXmight get lost (downstream of altered splice site)
379390HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1179 / 1179
position (AA) of stopcodon in wt / mu AA sequence 393 / 393
position of stopcodon in wt / mu cDNA 1226 / 1226
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 48 / 48
chromosome 6
strand 1
last intron/exon boundary 1235
theoretical NMD boundary in CDS 1137
length of CDS 1179
coding sequence (CDS) position 616
cDNA position
(for ins/del: last normal base / first normal base)		 663
gDNA position
(for ins/del: last normal base / first normal base)		 62367
chromosomal position
(for ins/del: last normal base / first normal base)		 80878730
original gDNA sequence snippet GTCCTGAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTA
altered gDNA sequence snippet GTCCTGAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTA
original cDNA sequence snippet GTCCTGAAGCATTTTTTGCCCATTGCCCAGGAATCAAGGTG
altered cDNA sequence snippet GTCCTGAAGCATTTTTTGCCTATTGCCCAGGAATCAAGGTG
wildtype AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAHCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
mutated AA sequence MAVVAAAAGW LLRLRAAGAE GHWRRLPGAG LARGFLHPAA TVEDAAQRRQ VAHFTFQPDP
EPREYGQTQK MNLFQSVTSA LDNSLAKDPT AVIFGEDVAF GGVFRCTVGL RDKYGKDRVF
NTPLCEQGIV GFGIGIAVTG ATAIAEIQFA DYIFPAFDQI VNEAAKYRYR SGDLFNCGSL
TIRSPWGCVG HGALYHSQSP EAFFAYCPGI KVVIPRSPFQ AKGLLLSCIE DKNPCIFFEP
KILYRAAAEE VPIEPYNIPL SQAEVIQEGS DVTLVAWGTQ VHVIREVASM AKEKLGVSCE
VIDLRTIIPW DVDTICKSVI KTGRLLISHE APLTGGFASE ISSTVQEECF LNLEAPISRV
CGYDTPFPHI FEPFYIPDKW KCYDALRKMI NY*
speed 1.24 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