Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999985731712571 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980216)
  • known disease mutation: rs37392 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:41267761C>TN/A show variant in all transcripts   IGV
HGNC symbol BRCA1
Ensembl transcript ID ENST00000351666
Genbank transcript ID N/A
UniProt peptide P38398
alteration type single base exchange
alteration region CDS
DNA changes c.116G>A
cDNA.135G>A
g.54530G>A
AA changes C39Y Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs80357498
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs37392 (pathogenic for Breast neoplasm|Hereditary breast and ovarian cancer syndrome|Breast-ovarian cancer, familial 1|Hereditary cancer-predisposing syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980216)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980216)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980216)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9151
3.4531
(flanking)2.9020.975
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained545260.64mu: CCACAAAGTATGACC ACAA|agta
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39LELIKEPVSTKCDHIFCKFCMLKL
mutated  not conserved    39LELIKEPVSTKYDHIFCKFCMLK
Ptroglodytes  all identical  ENSPTRG00000009236  39LELIKEPVSTKCDHIFCKFCMLK
Mmulatta  all identical  ENSMMUG00000001329  39LELIKEPVSTKCDHIFCRFCMLK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000017146  39LELIKEPVSTKCDHIFCKFCMLK
Ggallus  all identical  ENSGALG00000002781  39LDVIKEPVSTKCDHVFCRFCMFK
Trubripes  all identical  ENSTRUG00000009091  37LDILTAPVSTKCDHQFCKFCISK
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024564  39LELMKEPVATKCDHIFCKFCMLQ
protein features
start (aa)end (aa)featuredetails 
2465ZN_FINGRING-type.lost
4653HELIXmight get lost (downstream of altered splice site)
5458STRANDmight get lost (downstream of altered splice site)
6264TURNmight get lost (downstream of altered splice site)
7072TURNmight get lost (downstream of altered splice site)
7171MUTAGENR->G: No effect on interaction with BAP1.might get lost (downstream of altered splice site)
7880STRANDmight get lost (downstream of altered splice site)
8196HELIXmight get lost (downstream of altered splice site)
8989CONFLICTI -> T (in Ref. 4; AAB61673).might get lost (downstream of altered splice site)
148148CONFLICTMissing (in Ref. 4; AAB61673).might get lost (downstream of altered splice site)
253253CONFLICTA -> V (in Ref. 3; AAC00049).might get lost (downstream of altered splice site)
308308MOD_RESPhosphoserine; by AURKA.might get lost (downstream of altered splice site)
308308MUTAGENS->N: Abolishes phosphorylation by AURKA and interferes with cell cycle progression from G2 to mitosis.might get lost (downstream of altered splice site)
395395MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
398398MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
403403MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
651654COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
753753MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
840840MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
988988MOD_RESPhosphoserine; by CHEK2.might get lost (downstream of altered splice site)
10771077CONFLICTG -> R (in Ref. 4; AAB61673).might get lost (downstream of altered splice site)
11431143MUTAGENS->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
11431143MOD_RESPhosphoserine; by ATR; in vitro.might get lost (downstream of altered splice site)
12111211MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12121212MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12171217MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12181218MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12391239MUTAGENS->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
12391239MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12451245MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
12801280MOD_RESPhosphoserine; by ATR; in vitro.might get lost (downstream of altered splice site)
12801280MUTAGENS->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
12981298MUTAGENS->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
13301330MUTAGENS->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
13301330MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13361336MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13421342MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13871387MOD_RESPhosphoserine; by ATM and ATR.might get lost (downstream of altered splice site)
13871387MUTAGENS->A: Loss of IR-induced S-phase checkpoint. Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
13941394MUTAGENT->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
13941394MOD_RESPhosphothreonine; by ATR; in vitro.might get lost (downstream of altered splice site)
13971424REGIONInteraction with PALB2.might get lost (downstream of altered splice site)
14231423MOD_RESPhosphoserine; by ATM and ATR.might get lost (downstream of altered splice site)
14231423MUTAGENS->A: Inhibition of the infrared-induced G2 arrest. Reduces phosphorylation by ATR.might get lost (downstream of altered splice site)
14261426CONFLICTS -> P (in Ref. 3; AAC00049).might get lost (downstream of altered splice site)
14531453CONFLICTMissing (in Ref. 3; AAC00049).might get lost (downstream of altered splice site)
14571457MOD_RESPhosphoserine; by ATR; in vitro.might get lost (downstream of altered splice site)
14571457MUTAGENS->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
14661466MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
14661466MUTAGENS->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
15241524MUTAGENS->A: No change in infrared S-phase delay; when associated with A-1387. No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
15241524MOD_RESPhosphoserine; by ATM.might get lost (downstream of altered splice site)
15421542MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
16421736DOMAINBRCT 1.might get lost (downstream of altered splice site)
16511656STRANDmight get lost (downstream of altered splice site)
16551655MUTAGENS->A: Abolishes interaction with BRIP1.might get lost (downstream of altered splice site)
16591672HELIXmight get lost (downstream of altered splice site)
16751679STRANDmight get lost (downstream of altered splice site)
16861689STRANDmight get lost (downstream of altered splice site)
16951697STRANDmight get lost (downstream of altered splice site)
17001700MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
17011708HELIXmight get lost (downstream of altered splice site)
17021702MUTAGENK->M: Abolishes interaction with BRIP1.might get lost (downstream of altered splice site)
17121715STRANDmight get lost (downstream of altered splice site)
17171724HELIXmight get lost (downstream of altered splice site)
17201720MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
17201720MUTAGENT->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
17251727STRANDmight get lost (downstream of altered splice site)
17311734HELIXmight get lost (downstream of altered splice site)
17381738MUTAGENG->E: Abolishes interaction with BRIP1.might get lost (downstream of altered splice site)
17401742TURNmight get lost (downstream of altered splice site)
17431745STRANDmight get lost (downstream of altered splice site)
17481753HELIXmight get lost (downstream of altered splice site)
17551755MUTAGENS->A: No effect on in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
17551757TURNmight get lost (downstream of altered splice site)
17561855DOMAINBRCT 2.might get lost (downstream of altered splice site)
17601763TURNmight get lost (downstream of altered splice site)
17651768STRANDmight get lost (downstream of altered splice site)
17701772STRANDmight get lost (downstream of altered splice site)
17731775STRANDmight get lost (downstream of altered splice site)
17771786HELIXmight get lost (downstream of altered splice site)
17891791STRANDmight get lost (downstream of altered splice site)
17951797HELIXmight get lost (downstream of altered splice site)
18011803STRANDmight get lost (downstream of altered splice site)
18061810STRANDmight get lost (downstream of altered splice site)
18121814HELIXmight get lost (downstream of altered splice site)
18191822HELIXmight get lost (downstream of altered splice site)
18251827TURNmight get lost (downstream of altered splice site)
18281830STRANDmight get lost (downstream of altered splice site)
18321834STRANDmight get lost (downstream of altered splice site)
18351844HELIXmight get lost (downstream of altered splice site)
18511853HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2043 / 2043
position (AA) of stopcodon in wt / mu AA sequence 681 / 681
position of stopcodon in wt / mu cDNA 2062 / 2062
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 20 / 20
chromosome 17
strand -1
last intron/exon boundary 1938
theoretical NMD boundary in CDS 1868
length of CDS 2043
coding sequence (CDS) position 116
cDNA position
(for ins/del: last normal base / first normal base)		 135
gDNA position
(for ins/del: last normal base / first normal base)		 54530
chromosomal position
(for ins/del: last normal base / first normal base)		 41267761
original gDNA sequence snippet GGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAGT
altered gDNA sequence snippet GGAACCTGTCTCCACAAAGTATGACCACATATTTTGCAAGT
original cDNA sequence snippet GGAACCTGTCTCCACAAAGTGTGACCACATATTTTGCAAAT
altered cDNA sequence snippet GGAACCTGTCTCCACAAAGTATGACCACATATTTTGCAAAT
wildtype AA sequence MDLSALRVEE VQNVINAMQK ILECPICLEL IKEPVSTKCD HIFCKFCMLK LLNQKKGPSQ
CPLCKNDITK RSLQESTRFS QLVEELLKII CAFQLDTGLE YANSYNFAKK ENNSPEHLKD
EVSIIQSMGY RNRAKRLLQS EPENPSLQET SLSVQLSNLG TVRTLRTKQR IQPQKTSVYI
ELGEAASGCE SETSVSEDCS GLSSQSDILT TQQRDTMQHN LIKLQQEMAE LEAVLEQHGS
QPSNSYPSII SDSSALEDLR NPEQSTSEKA VLTSQKSSEY PISQNPEGLS ADKFEVSADS
STSKNKEPGV ERSSPSKCPS LDDRWYMHSC SGSLQNRNYP SQEELIKVVD VEEQQLEESG
PHDLTETSYL PRQDLEGTPY LESGISLFSD DPESDPSEDR APESARVGNI PSSTSALKVP
QLKVAESAQS PAAAHTTDTA GYNAMEESVS REKPELTAST ERVNKRMSMV VSGLTPEEFM
LVYKFARKHH ITLTNLITEE TTHVVMKTDA EFVCERTLKY FLGIAGGKWV VSYFWVTQSI
KERKMLNEHD FEVRGDVVNG RNHQGPKRAR ESQDRKIFRG LEICCYGPFT NMPTDQLEWM
VQLCGASVVK ELSSFTLGTG VHPIVVVQPD AWTEDNGFHA IGQMCEAPVV TREWVLDSVA
LYQCQELDTY LIPQIPHSHY *
mutated AA sequence MDLSALRVEE VQNVINAMQK ILECPICLEL IKEPVSTKYD HIFCKFCMLK LLNQKKGPSQ
CPLCKNDITK RSLQESTRFS QLVEELLKII CAFQLDTGLE YANSYNFAKK ENNSPEHLKD
EVSIIQSMGY RNRAKRLLQS EPENPSLQET SLSVQLSNLG TVRTLRTKQR IQPQKTSVYI
ELGEAASGCE SETSVSEDCS GLSSQSDILT TQQRDTMQHN LIKLQQEMAE LEAVLEQHGS
QPSNSYPSII SDSSALEDLR NPEQSTSEKA VLTSQKSSEY PISQNPEGLS ADKFEVSADS
STSKNKEPGV ERSSPSKCPS LDDRWYMHSC SGSLQNRNYP SQEELIKVVD VEEQQLEESG
PHDLTETSYL PRQDLEGTPY LESGISLFSD DPESDPSEDR APESARVGNI PSSTSALKVP
QLKVAESAQS PAAAHTTDTA GYNAMEESVS REKPELTAST ERVNKRMSMV VSGLTPEEFM
LVYKFARKHH ITLTNLITEE TTHVVMKTDA EFVCERTLKY FLGIAGGKWV VSYFWVTQSI
KERKMLNEHD FEVRGDVVNG RNHQGPKRAR ESQDRKIFRG LEICCYGPFT NMPTDQLEWM
VQLCGASVVK ELSSFTLGTG VHPIVVVQPD AWTEDNGFHA IGQMCEAPVV TREWVLDSVA
LYQCQELDTY LIPQIPHSHY *
speed 0.31 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