Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999999 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032859)
  • known disease mutation: rs6555 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:96051026T>AN/A show variant in all transcripts   IGV
HGNC symbol BMPR1B
Ensembl transcript ID ENST00000440890
Genbank transcript ID N/A
UniProt peptide O00238
alteration type single base exchange
alteration region CDS
DNA changes c.689T>A
cDNA.710T>A
g.371908T>A
AA changes I230K Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 230
frameshift no
known variant Reference ID: rs121434417
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6555 (pathogenic for Brachydactyly type A2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032859)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032859)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032859)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H2AZ, Histone, Histone 2A variant Z
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)5.1190.999
5.1191
(flanking)0.1440.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased371909wt: 0.9986 / mu: 0.9992 (marginal change - not scored)wt: ACTATAGCTAAGCAG
mu: ACTAAAGCTAAGCAG		 TATA|gcta
Donor gained3719040.99mu: AAAGGACTAAAGCTA AGGA|ctaa
distance from splice site 14
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      230GSGLPLLVQRTIAKQIQMVKQIGK
mutated  not conserved    230GSGLPLLVQRTKAKQIQMVKQI
Ptroglodytes  all identical  ENSPTRG00000016293  229GSGLPLLVQRTIAKQIQMVKQI
Mmulatta  all identical  ENSMMUG00000006702  200GSGLPLLVQRTIAKQIQMVKQIG
Fcatus  no alignment  ENSFCAG00000015084  n/a
Mmusculus  all identical  ENSMUSG00000052430  200GSGLPLLVQRTIAKQIQMVKQIG
Ggallus  all identical  ENSGALG00000012216  233GSGLPLLVQRTIAKQIQMVKQI
Trubripes  all identical  ENSTRUG00000013761  231GSGLPLLVQRTIAKQIQMVKQI
Drerio  all identical  ENSDARG00000031219  52GSGLPLLVQRTIAKQIQMVK
Dmelanogaster  all identical  FBgn0003716  269GSGLPLLVQRTIAKQIQMVRLVG
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019220  230GSGLPLLVQRTIAKQIQMVKQI
protein features
start (aa)end (aa)featuredetails 
149502TOPO_DOMCytoplasmic (Potential).lost
204494DOMAINProtein kinase.lost
226234STRANDlost
231231BINDINGATP (By similarity).might get lost (downstream of altered splice site)
235237HELIXmight get lost (downstream of altered splice site)
238248HELIXmight get lost (downstream of altered splice site)
261268STRANDmight get lost (downstream of altered splice site)
270272HELIXmight get lost (downstream of altered splice site)
274279STRANDmight get lost (downstream of altered splice site)
287293HELIXmight get lost (downstream of altered splice site)
298316HELIXmight get lost (downstream of altered splice site)
332332ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
337340STRANDmight get lost (downstream of altered splice site)
346348STRANDmight get lost (downstream of altered splice site)
375377HELIXmight get lost (downstream of altered splice site)
380383HELIXmight get lost (downstream of altered splice site)
393411HELIXmight get lost (downstream of altered splice site)
426430TURNmight get lost (downstream of altered splice site)
437444HELIXmight get lost (downstream of altered splice site)
455459HELIXmight get lost (downstream of altered splice site)
461473HELIXmight get lost (downstream of altered splice site)
478480HELIXmight get lost (downstream of altered splice site)
484496HELIXmight get lost (downstream of altered splice site)
497499TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1599 / 1599
position (AA) of stopcodon in wt / mu AA sequence 533 / 533
position of stopcodon in wt / mu cDNA 1620 / 1620
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 22 / 22
chromosome 4
strand 1
last intron/exon boundary 1495
theoretical NMD boundary in CDS 1423
length of CDS 1599
coding sequence (CDS) position 689
cDNA position
(for ins/del: last normal base / first normal base)		 710
gDNA position
(for ins/del: last normal base / first normal base)		 371908
chromosomal position
(for ins/del: last normal base / first normal base)		 96051026
original gDNA sequence snippet TTCACAGGTCCAAAGGACTATAGCTAAGCAGATTCAGATGG
altered gDNA sequence snippet TTCACAGGTCCAAAGGACTAAAGCTAAGCAGATTCAGATGG
original cDNA sequence snippet TCTGCTGGTCCAAAGGACTATAGCTAAGCAGATTCAGATGG
altered cDNA sequence snippet TCTGCTGGTCCAAAGGACTAAAGCTAAGCAGATTCAGATGG
wildtype AA sequence MGWLEELNWQ LHIFLLILLS MHTRANFLDN MLLRSAGKLN VGTKKEDGES TAPTPRPKVL
RCKCHHHCPE DSVNNICSTD GYCFTMIEED DSGLPVVTSG CLGLEGSDFQ CRDTPIPHQR
RSIECCTERN ECNKDLHPTL PPLKNRDFVD GPIHHRALLI SVTVCSLLLV LIILFCYFRY
KRQETRPRYS IGLEQDETYI PPGESLRDLI EQSQSSGSGS GLPLLVQRTI AKQIQMVKQI
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDY LKSTTLDAKS MLKLAYSSVS GLCHLHTEIF STQGKPAIAH
RDLKSKNILV KKNGTCCIAD LGLAVKFISD TNEVDIPPNT RVGTKRYMPP EVLDESLNRN
HFQSYIMADM YSFGLILWEV ARRCVSGGIV EEYQLPYHDL VPSDPSYEDM REIVCIKKLR
PSFPNRWSSD ECLRQMGKLM TECWAHNPAS RLTALRVKKT LAKMSESQDI KL*
mutated AA sequence MGWLEELNWQ LHIFLLILLS MHTRANFLDN MLLRSAGKLN VGTKKEDGES TAPTPRPKVL
RCKCHHHCPE DSVNNICSTD GYCFTMIEED DSGLPVVTSG CLGLEGSDFQ CRDTPIPHQR
RSIECCTERN ECNKDLHPTL PPLKNRDFVD GPIHHRALLI SVTVCSLLLV LIILFCYFRY
KRQETRPRYS IGLEQDETYI PPGESLRDLI EQSQSSGSGS GLPLLVQRTK AKQIQMVKQI
GKGRYGEVWM GKWRGEKVAV KVFFTTEEAS WFRETEIYQT VLMRHENILG FIAADIKGTG
SWTQLYLITD YHENGSLYDY LKSTTLDAKS MLKLAYSSVS GLCHLHTEIF STQGKPAIAH
RDLKSKNILV KKNGTCCIAD LGLAVKFISD TNEVDIPPNT RVGTKRYMPP EVLDESLNRN
HFQSYIMADM YSFGLILWEV ARRCVSGGIV EEYQLPYHDL VPSDPSYEDM REIVCIKKLR
PSFPNRWSSD ECLRQMGKLM TECWAHNPAS RLTALRVKKT LAKMSESQDI KL*
speed 0.17 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