Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM058359)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:41244000T>CN/A show variant in all transcripts   IGV
HGNC symbol BRCA1
Ensembl transcript ID ENST00000309486
Genbank transcript ID N/A
UniProt peptide P38398
alteration type single base exchange
alteration region CDS
DNA changes c.2660A>G
cDNA.3688A>G
g.78291A>G
AA changes K887R Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 887
frameshift no
known variant Reference ID: rs16942
databasehomozygous (C/C)heterozygousallele carriers
1000G35210621414
ExAC77681723124999

known disease mutation at this position, please check HGMD for details (HGMD ID CM058359)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.5470.001
-0.6840
(flanking)0.5580.001
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 increased78288wt: 0.9731 / mu: 0.9762 (marginal change - not scored)wt: CGTCCAGAAAGGAGA
mu: CGTCCAGAGAGGAGA		 TCCA|gaaa
Donor increased78290wt: 0.88 / mu: 1.00wt: TCCAGAAAGGAGAGC
mu: TCCAGAGAGGAGAGC		 CAGA|aagg
Donor gained782850.62mu: AAGCGTCCAGAGAGG GCGT|ccag
distance from splice site 549
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      887ESSAVFSKSVQKGELSRSPSPFTH
mutated  all conserved    887ESSAVFSKSVQRGELSRSPSPFT
Ptroglodytes  all conserved  ENSPTRG00000009236  1183ESSAVFSKSVQRGELSRSPSPFT
Mmulatta  all conserved  ENSMMUG00000001329  1183ESSAVFSKSIQRGELSRSPSPFT
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000017146  1147ERSAVFNGSILRRESSRSPSPV
Ggallus  not conserved  ENSGALG00000002781  1180DTSAVFVKRSGAAWVKEVNDSVVSCKP----
Trubripes  no alignment  ENSTRUG00000009091  n/a
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000024564  965--KNAAHPE-SFLPSSVH
protein features
start (aa)end (aa)featuredetails 
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)
12801280MUTAGENS->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
12801280MOD_RESPhosphoserine; by ATR; in vitro.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)
13301330MOD_RESPhosphoserine.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)
13361336MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
13421342MOD_RESPhosphoserine.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)
13871387MOD_RESPhosphoserine; by ATM and ATR.might get lost (downstream of altered splice site)
13941394MOD_RESPhosphothreonine; by ATR; in vitro.might get lost (downstream of altered splice site)
13941394MUTAGENT->A: Reduces in vitro phosphorylation by ATR.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)
14571457MUTAGENS->A: Reduces in vitro phosphorylation by ATR.might get lost (downstream of altered splice site)
14571457MOD_RESPhosphoserine; by ATR; in vitro.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 4704 / 4704
position (AA) of stopcodon in wt / mu AA sequence 1568 / 1568
position of stopcodon in wt / mu cDNA 5732 / 5732
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 1029 / 1029
chromosome 17
strand -1
last intron/exon boundary 5608
theoretical NMD boundary in CDS 4529
length of CDS 4704
coding sequence (CDS) position 2660
cDNA position
(for ins/del: last normal base / first normal base)		 3688
gDNA position
(for ins/del: last normal base / first normal base)		 78291
chromosomal position
(for ins/del: last normal base / first normal base)		 41244000
original gDNA sequence snippet TTTTAGCAAAAGCGTCCAGAAAGGAGAGCTTAGCAGGAGTC
altered gDNA sequence snippet TTTTAGCAAAAGCGTCCAGAGAGGAGAGCTTAGCAGGAGTC
original cDNA sequence snippet TTTTAGCAAAAGCGTCCAGAAAGGAGAGCTTAGCAGGAGTC
altered cDNA sequence snippet TTTTAGCAAAAGCGTCCAGAGAGGAGAGCTTAGCAGGAGTC
wildtype AA sequence MNVEKAEFCN KSKQPGLARS QHNRWAGSKE TCNDRRTPST EKKVDLNADP LCERKEWNKQ
KLPCSENPRD TEDVPWITLN SSIQKVNEWF SRSDELLGSD DSHDGESESN AKVADVLDVL
NEVDEYSGSS EKIDLLASDP HEALICKSER VHSKSVESNI EDKIFGKTYR KKASLPNLSH
VTENLIIGAF VTEPQIIQER PLTNKLKRKR RPTSGLHPED FIKKADLAVQ KTPEMINQGT
NQTEQNGQVM NITNSGHENK TKGDSIQNEK NPNPIESLEK ESAFKTKAEP ISSSISNMEL
ELNIHNSKAP KKNRLRRKSS TRHIHALELV VSRNLSPPNC TELQIDSCSS SEEIKKKKYN
QMPVRHSRNL QLMEGKEPAT GAKKSNKPNE QTSKRHDSDT FPELKLTNAP GSFTKCSNTS
ELKEFVNPSL PREEKEEKLE TVKVSNNAED PKDLMLSGER VLQTERSVES SSISLVPGTD
YGTQESISLL EVSTLGKAKT EPNKCVSQCA AFENPKGLIH GCSKDNRNDT EGFKYPLGHE
VNHSRETSIE MEESELDAQY LQNTFKVSKR QSFAPFSNPG NAEEECATFS AHSGSLKKQS
PKVTFECEQK EENQGKNESN IKPVQTVNIT AGFPVVGQKD KPVDNAKCSI KGGSRFCLSS
QFRGNETGLI TPNKHGLLQN PYRIPPLFPI KSFVKTKCKK NLLEENFEEH SMSPEREMGN
ENIPSTVSTI SRNNIRENVF KEASSSNINE VGSSTNEVGS SINEIGSSDE NIQAELGRNR
GPKLNAMLRL GVLQPEVYKQ SLPGSNCKHP EIKKQEYEEV VQTVNTDFSP YLISDNLEQP
MGSSHASQVC SETPDDLLDD GEIKEDTSFA ENDIKESSAV FSKSVQKGEL SRSPSPFTHT
HLAQGYRRGA KKLESSEENL SSEDEELPCF QHLLFGKVNN IPSQSTRHST VATECLSKNT
EENLLSLKNS LNDCSNQVIL AKASQEHHLS EETKCSASLF SSQCSELEDL TANTNTQDPF
LIGSSKQMRH QSESQGVGLS DKELVSDDEE RGTGLEENNQ EEQSMDSNLG EAASGCESET
SVSEDCSGLS SQSDILTTQQ RDTMQHNLIK LQQEMAELEA VLEQHGSQPS NSYPSIISDS
SALEDLRNPE QSTSEKAVLT SQKSSEYPIS QNPEGLSADK FEVSADSSTS KNKEPGVERS
SPSKCPSLDD RWYMHSCSGS LQNRNYPSQE ELIKVVDVEE QQLEESGPHD LTETSYLPRQ
DLEGTPYLES GISLFSDDPE SDPSEDRAPE SARVGNIPSS TSALKVPQLK VAESAQSPAA
AHTTDTAGYN AMEESVSREK PELTASTERV NKRMSMVVSG LTPEEFMLVY KFARKHHITL
TNLITEETTH VVMKTDAEFV CERTLKYFLG IAGGKWVVSY FWVTQSIKER KMLNEHDFEV
RGDVVNGRNH QGPKRARESQ DRKIFRGLEI CCYGPFTNMP TDQLEWMVQL CGASVVKELS
SFTLGTGVHP IVVVQPDAWT EDNGFHAIGQ MCEAPVVTRE WVLDSVALYQ CQELDTYLIP
QIPHSHY*
mutated AA sequence MNVEKAEFCN KSKQPGLARS QHNRWAGSKE TCNDRRTPST EKKVDLNADP LCERKEWNKQ
KLPCSENPRD TEDVPWITLN SSIQKVNEWF SRSDELLGSD DSHDGESESN AKVADVLDVL
NEVDEYSGSS EKIDLLASDP HEALICKSER VHSKSVESNI EDKIFGKTYR KKASLPNLSH
VTENLIIGAF VTEPQIIQER PLTNKLKRKR RPTSGLHPED FIKKADLAVQ KTPEMINQGT
NQTEQNGQVM NITNSGHENK TKGDSIQNEK NPNPIESLEK ESAFKTKAEP ISSSISNMEL
ELNIHNSKAP KKNRLRRKSS TRHIHALELV VSRNLSPPNC TELQIDSCSS SEEIKKKKYN
QMPVRHSRNL QLMEGKEPAT GAKKSNKPNE QTSKRHDSDT FPELKLTNAP GSFTKCSNTS
ELKEFVNPSL PREEKEEKLE TVKVSNNAED PKDLMLSGER VLQTERSVES SSISLVPGTD
YGTQESISLL EVSTLGKAKT EPNKCVSQCA AFENPKGLIH GCSKDNRNDT EGFKYPLGHE
VNHSRETSIE MEESELDAQY LQNTFKVSKR QSFAPFSNPG NAEEECATFS AHSGSLKKQS
PKVTFECEQK EENQGKNESN IKPVQTVNIT AGFPVVGQKD KPVDNAKCSI KGGSRFCLSS
QFRGNETGLI TPNKHGLLQN PYRIPPLFPI KSFVKTKCKK NLLEENFEEH SMSPEREMGN
ENIPSTVSTI SRNNIRENVF KEASSSNINE VGSSTNEVGS SINEIGSSDE NIQAELGRNR
GPKLNAMLRL GVLQPEVYKQ SLPGSNCKHP EIKKQEYEEV VQTVNTDFSP YLISDNLEQP
MGSSHASQVC SETPDDLLDD GEIKEDTSFA ENDIKESSAV FSKSVQRGEL SRSPSPFTHT
HLAQGYRRGA KKLESSEENL SSEDEELPCF QHLLFGKVNN IPSQSTRHST VATECLSKNT
EENLLSLKNS LNDCSNQVIL AKASQEHHLS EETKCSASLF SSQCSELEDL TANTNTQDPF
LIGSSKQMRH QSESQGVGLS DKELVSDDEE RGTGLEENNQ EEQSMDSNLG EAASGCESET
SVSEDCSGLS SQSDILTTQQ RDTMQHNLIK LQQEMAELEA VLEQHGSQPS NSYPSIISDS
SALEDLRNPE QSTSEKAVLT SQKSSEYPIS QNPEGLSADK FEVSADSSTS KNKEPGVERS
SPSKCPSLDD RWYMHSCSGS LQNRNYPSQE ELIKVVDVEE QQLEESGPHD LTETSYLPRQ
DLEGTPYLES GISLFSDDPE SDPSEDRAPE SARVGNIPSS TSALKVPQLK VAESAQSPAA
AHTTDTAGYN AMEESVSREK PELTASTERV NKRMSMVVSG LTPEEFMLVY KFARKHHITL
TNLITEETTH VVMKTDAEFV CERTLKYFLG IAGGKWVVSY FWVTQSIKER KMLNEHDFEV
RGDVVNGRNH QGPKRARESQ DRKIFRGLEI CCYGPFTNMP TDQLEWMVQL CGASVVKELS
SFTLGTGVHP IVVVQPDAWT EDNGFHAIGQ MCEAPVVTRE WVLDSVALYQ CQELDTYLIP
QIPHSHY*
speed 1.31 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