Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999891114268 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CD050129)
  • known disease mutation at this position (HGMD CM970049)
  • known disease mutation: rs8249 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:52309891C>TN/A show variant in all transcripts   IGV
HGNC symbol ACVRL1
Ensembl transcript ID ENST00000550683
Genbank transcript ID N/A
UniProt peptide P37023
alteration type single base exchange
alteration region CDS
DNA changes c.1162C>T
cDNA.1263C>T
g.9200C>T
AA changes R388W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 388
frameshift no
known variant Reference ID: rs28936401
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8249 (pathogenic for Telangiectasia, hereditary hemorrhagic, type 2|Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)

known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970049)

known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970049)
known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)

known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970049)
known disease mutation at this position, please check HGMD for details (HGMD ID CD050129)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970049)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.2191
0.8191
(flanking)5.8781
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased9193wt: 0.68 / mu: 0.96wt: GTGGGCACCAAGCGG
mu: GTGGGCACCAAGTGG		 GGGC|acca
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      388DIGNNPRVGTKRYMAPEVLDEQIR
mutated  not conserved    388DIGNNPRVGTKWYMAPEVLDEQI
Ptroglodytes  all identical  ENSPTRG00000004963  374DIGNNPRVGTKRYMAPEVLDEQI
Mmulatta  all identical  ENSMMUG00000004982  381DIGNNPRVGTKRYMAPEVLDEQI
Fcatus  all identical  ENSFCAG00000000265  376DIGNNPRVGTKRYMAPEVLEEQI
Mmusculus  all identical  ENSMUSG00000000530  373DIGNNPRVGTKRYMAPEVLDEHI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000012725  341DVGNNPRVGTKRYMAPEVLDETI
Drerio  all identical  ENSDARG00000018179  369DVGTNPRVGTKRYMAPEVLDETI
Dmelanogaster  all identical  FBgn0003317  436DLGNNPKVGTKRYMAPEVLDESI
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000031897  344DIGNNPRVGTKRYMAPEVLDETI
protein features
start (aa)end (aa)featuredetails 
142503TOPO_DOMCytoplasmic (Potential).lost
202492DOMAINProtein kinase.lost
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 1554 / 1554
position (AA) of stopcodon in wt / mu AA sequence 518 / 518
position of stopcodon in wt / mu cDNA 1655 / 1655
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 102 / 102
chromosome 12
strand 1
last intron/exon boundary 1521
theoretical NMD boundary in CDS 1369
length of CDS 1554
coding sequence (CDS) position 1162
cDNA position
(for ins/del: last normal base / first normal base)		 1263
gDNA position
(for ins/del: last normal base / first normal base)		 9200
chromosomal position
(for ins/del: last normal base / first normal base)		 52309891
original gDNA sequence snippet ACCCGAGAGTGGGCACCAAGCGGTACATGGCACCCGAGGTG
altered gDNA sequence snippet ACCCGAGAGTGGGCACCAAGTGGTACATGGCACCCGAGGTG
original cDNA sequence snippet ACCCGAGAGTGGGCACCAAGCGGTACATGGCACCCGAGGTG
altered cDNA sequence snippet ACCCGAGAGTGGGCACCAAGTGGTACATGGCACCCGAGGTG
wildtype AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGDPVKP SRGPLVTCTC ESPHCKGPTC
RGAWCTVVLV REEGRHPQEH RGCGNLHREL CRGRPTEFVN HYCCDSHLCN HNVSLVLEAT
QPPSEQPGTD GQLALILGPV LALLALVALG VLGLWHVRRR QEKQRGLHSE LGESSLILKA
SEQGDSMLGD LLDSDCTTGS GSGLPFLVQR TVARQVALVE CVGKGRYGEV WRGLWHGESV
AVKIFSSRDE QSWFRETEIY NTVLLRHDNI LGFIASDMTS RNSSTQLWLI THYHEHGSLY
DFLQRQTLEP HLALRLAVSA ACGLAHLHVE IFGTQGKPAI AHRDFKSRNV LVKSNLQCCI
ADLGLAVMHS QGSDYLDIGN NPRVGTKRYM APEVLDEQIR TDCFESYKWT DIWAFGLVLW
EIARRTIVNG IVEDYRPPFY DVVPNDPSFE DMKKVVCVDQ QTPTIPNRLA ADPVLSGLAQ
MMRECWYPNP SARLTALRIK KTLQKISNSP EKPKVIQ*
mutated AA sequence MALTPPLLLL SAGTMTLGSP RKGLLMLLMA LVTQGDPVKP SRGPLVTCTC ESPHCKGPTC
RGAWCTVVLV REEGRHPQEH RGCGNLHREL CRGRPTEFVN HYCCDSHLCN HNVSLVLEAT
QPPSEQPGTD GQLALILGPV LALLALVALG VLGLWHVRRR QEKQRGLHSE LGESSLILKA
SEQGDSMLGD LLDSDCTTGS GSGLPFLVQR TVARQVALVE CVGKGRYGEV WRGLWHGESV
AVKIFSSRDE QSWFRETEIY NTVLLRHDNI LGFIASDMTS RNSSTQLWLI THYHEHGSLY
DFLQRQTLEP HLALRLAVSA ACGLAHLHVE IFGTQGKPAI AHRDFKSRNV LVKSNLQCCI
ADLGLAVMHS QGSDYLDIGN NPRVGTKWYM APEVLDEQIR TDCFESYKWT DIWAFGLVLW
EIARRTIVNG IVEDYRPPFY DVVPNDPSFE DMKKVVCVDQ QTPTIPNRLA ADPVLSGLAQ
MMRECWYPNP SARLTALRIK KTLQKISNSP EKPKVIQ*
speed 1.22 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