Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999985008 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033590)
  • known disease mutation at this position (HGMD CM060197)
  • known disease mutation: rs8253 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52308229G>AN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000419526
Genbank transcript ID N/A
UniProt peptide P37023
alteration type single base exchange
alteration region CDS
DNA changes c.110G>A
cDNA.172G>A
g.7538G>A
AA changes G37D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 37
frameshift no
known variant Reference ID: rs28936687
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8253 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2|Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033590)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060197)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9411
5.5361
(flanking)0.2630.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc decreased7531wt: 0.69 / mu: 0.55wt: ACCTTCCCCTCTGGCCATCAGGAAAAGGCCGCTATGGCGAA
mu: ACCTTCCCCTCTGGCCATCAGGAAAAGACCGCTATGGCGAA		 tcag|GAAA
Donor marginally increased7540wt: 0.9350 / mu: 0.9830 (marginal change - not scored)wt: AAGGCCGCTATGGCG
mu: AAGACCGCTATGGCG		 GGCC|gcta
Donor marginally increased7530wt: 0.9899 / mu: 0.9974 (marginal change - not scored)wt: CCATCAGGAAAAGGC
mu: CCATCAGGAAAAGAC		 ATCA|ggaa
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      37MLLMALVTQGKGRYGEVWRGLWHG
mutated  not conserved    37MLLMALVTQGKDRYGEVWRGLWH
Ptroglodytes  all identical  ENSPTRG00000004963  211GKGRYGEVWRGLWH
Mmulatta  all identical  ENSMMUG00000004982  211GKGRYGEVWRGLWH
Fcatus  all identical  ENSFCAG00000000265  213GKGRYGEVWRGLWH
Mmusculus  all identical  ENSMUSG00000000530  210GKGRYGEVWRGSWH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  178GKGRYGEVWRGTWM
Drerio  all identical  ENSDARG00000018179  206GKGRYGEVWRGTWM
Dmelanogaster  all identical  FBgn0003317  273GRGKYGEVWRGHWH
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031897  181GKGRYGEVWRGTWQ
protein features
start (aa)end (aa)featuredetails 
22118TOPO_DOMExtracellular (Potential).lost
3235STRANDmight get lost (downstream of altered splice site)
4256STRANDmight get lost (downstream of altered splice site)
5961STRANDmight get lost (downstream of altered splice site)
6468STRANDmight get lost (downstream of altered splice site)
7478HELIXmight get lost (downstream of altered splice site)
8390STRANDmight get lost (downstream of altered splice site)
9396TURNmight get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
119141TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
142503TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
155155MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
172172CONFLICTS -> T (in Ref. 1; CAA80255).might get lost (downstream of altered splice site)
172201DOMAINGS.might get lost (downstream of altered splice site)
198201HELIXmight get lost (downstream of altered splice site)
202492DOMAINProtein kinase.might get lost (downstream of altered splice site)
203211STRANDmight get lost (downstream of altered splice site)
208216NP_BINDATP (By similarity).might get lost (downstream of altered splice site)
214221STRANDmight get lost (downstream of altered splice site)
224231STRANDmight get lost (downstream of altered splice site)
229229BINDINGATP (By similarity).might get lost (downstream of altered splice site)
233235HELIXmight get lost (downstream of altered splice site)
236248HELIXmight get lost (downstream of altered splice site)
259265STRANDmight get lost (downstream of altered splice site)
272278STRANDmight get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
296314HELIXmight get lost (downstream of altered splice site)
325327STRANDmight get lost (downstream of altered splice site)
330330ACT_SITEProton acceptor (By similarity).might get lost (downstream of altered splice site)
335338STRANDmight get lost (downstream of altered splice site)
344346STRANDmight get lost (downstream of altered splice site)
353355STRANDmight get lost (downstream of altered splice site)
357359STRANDmight get lost (downstream of altered splice site)
373375HELIXmight get lost (downstream of altered splice site)
378381HELIXmight get lost (downstream of altered splice site)
390410HELIXmight get lost (downstream of altered splice site)
424428TURNmight get lost (downstream of altered splice site)
435442HELIXmight get lost (downstream of altered splice site)
455459STRANDmight get lost (downstream of altered splice site)
460462TURNmight get lost (downstream of altered splice site)
463469HELIXmight get lost (downstream of altered splice site)
476478HELIXmight get lost (downstream of altered splice site)
482491HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1052 / 1052
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 63 / 63
chromosome 12
strand 1
last intron/exon boundary 918
theoretical NMD boundary in CDS 805
length of CDS 990
coding sequence (CDS) position 110
cDNA position
(for ins/del: last normal base / first normal base)		 172
gDNA position
(for ins/del: last normal base / first normal base)		 7538
chromosomal position
(for ins/del: last normal base / first normal base)		 52308229
original gDNA sequence snippet CCTCTGGCCATCAGGAAAAGGCCGCTATGGCGAAGTGTGGC
altered gDNA sequence snippet CCTCTGGCCATCAGGAAAAGACCGCTATGGCGAAGTGTGGC
original cDNA sequence snippet CTTGGTGACCCAGGGAAAAGGCCGCTATGGCGAAGTGTGGC
altered cDNA sequence snippet CTTGGTGACCCAGGGAAAAGACCGCTATGGCGAAGTGTGGC
wildtype AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKGRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YMAPEVLDEQ IRTDCFESYK WTDIWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*
mutated AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGKDRYG EVWRGLWHGE SVAVKIFSSR
DEQSWFRETE IYNTVLLRHD NILGFIASDM TSRNSSTQLW LITHYHEHGS LYDFLQRQTL
EPHLALRLAV SAACGLAHLH VEIFGTQGKP AIAHRDFKSR NVLVKSNLQC CIADLGLAVM
HSQGSDYLDI GNNPRVGTKR YMAPEVLDEQ IRTDCFESYK WTDIWAFGLV LWEIARRTIV
NGIVEDYRPP FYDVVPNDPS FEDMKKVVCV DQQTPTIPNR LAADPVLSGL AQMMRECWYP
NPSARLTALR IKKTLQKISN SPEKPKVIQ*
speed 0.84 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