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MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000367429
MT speed 0 s - this script 7.906998 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CFHdisease_causing_automatic0.00152260267819769simple_aaeaffected0V1197Asingle base exchangers460184show file

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Prediction

disease causing

Model: simple_aae, prob: 0.00152260267819769 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010322)
  • known disease mutation: rs21090 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:196716337T>CN/A show variant in all transcripts   IGV
HGNC symbol CFH
Ensembl transcript ID ENST00000367429
Genbank transcript ID NM_000186
UniProt peptide P08603
alteration type single base exchange
alteration region CDS
DNA changes c.3590T>C
cDNA.3830T>C
g.95330T>C
AA changes V1197A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
1197
frameshift no
known variant Reference ID: rs460184
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs21090 (pathogenic for Atypical hemolytic-uremic syndrome 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010322)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010322)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010322)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5940.005
1.0170.771
(flanking)1.3090.966
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased95329wt: 0.28 / mu: 0.49wt: AATCAGTTGAATTTG
mu: AATCAGCTGAATTTG
 TCAG|ttga
Donor marginally increased95328wt: 0.8850 / mu: 0.8988 (marginal change - not scored)wt: GAATCAGTTGAATTT
mu: GAATCAGCTGAATTT
 ATCA|gttg
Donor gained953340.34mu: GCTGAATTTGTGTGT TGAA|tttg
distance from splice site 97
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1197KQKLYSRTGESVEFVCKRGYRLSS
mutated  not conserved    1197KQKLYSRTGESAEFV
Ptroglodytes  all identical  ENSPTRG00000001799  1197KEKIYSRTGESVEFI
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000026365  1220SGEDIEFGCKYGYYKA
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000092786  337PRKLFSPHKDQILFACLRENERMK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
11701230DOMAINSushi 20.lost
11961201STRANDlost
12011201DISULFIDBy similarity.might get lost (downstream of altered splice site)
12021204TURNmight get lost (downstream of altered splice site)
12051207STRANDmight get lost (downstream of altered splice site)
12141217STRANDmight get lost (downstream of altered splice site)
12181218DISULFIDBy similarity.might get lost (downstream of altered splice site)
12281228DISULFIDBy similarity.might get lost (downstream of altered splice site)
12281230STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3696 / 3696
position (AA) of stopcodon in wt / mu AA sequence 1232 / 1232
position of stopcodon in wt / mu cDNA 3936 / 3936
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 241 / 241
chromosome 1
strand 1
last intron/exon boundary 3734
theoretical NMD boundary in CDS 3443
length of CDS 3696
coding sequence (CDS) position 3590
cDNA position
(for ins/del: last normal base / first normal base)
3830
gDNA position
(for ins/del: last normal base / first normal base)
95330
chromosomal position
(for ins/del: last normal base / first normal base)
196716337
original gDNA sequence snippet TTCGAGAACAGGTGAATCAGTTGAATTTGTGTGTAAACGGG
altered gDNA sequence snippet TTCGAGAACAGGTGAATCAGCTGAATTTGTGTGTAAACGGG
original cDNA sequence snippet TTCGAGAACAGGTGAATCAGTTGAATTTGTGTGTAAACGGG
altered cDNA sequence snippet TTCGAGAACAGGTGAATCAGCTGAATTTGTGTGTAAACGGG
wildtype AA sequence MRLLAKIICL MLWAICVAED CNELPPRRNT EILTGSWSDQ TYPEGTQAIY KCRPGYRSLG
NVIMVCRKGE WVALNPLRKC QKRPCGHPGD TPFGTFTLTG GNVFEYGVKA VYTCNEGYQL
LGEINYRECD TDGWTNDIPI CEVVKCLPVT APENGKIVSS AMEPDREYHF GQAVRFVCNS
GYKIEGDEEM HCSDDGFWSK EKPKCVEISC KSPDVINGSP ISQKIIYKEN ERFQYKCNMG
YEYSERGDAV CTESGWRPLP SCEEKSCDNP YIPNGDYSPL RIKHRTGDEI TYQCRNGFYP
ATRGNTAKCT STGWIPAPRC TLKPCDYPDI KHGGLYHENM RRPYFPVAVG KYYSYYCDEH
FETPSGSYWD HIHCTQDGWS PAVPCLRKCY FPYLENGYNQ NHGRKFVQGK SIDVACHPGY
ALPKAQTTVT CMENGWSPTP RCIRVKTCSK SSIDIENGFI SESQYTYALK EKAKYQCKLG
YVTADGETSG SITCGKDGWS AQPTCIKSCD IPVFMNARTK NDFTWFKLND TLDYECHDGY
ESNTGSTTGS IVCGYNGWSD LPICYERECE LPKIDVHLVP DRKKDQYKVG EVLKFSCKPG
FTIVGPNSVQ CYHFGLSPDL PICKEQVQSC GPPPELLNGN VKEKTKEEYG HSEVVEYYCN
PRFLMKGPNK IQCVDGEWTT LPVCIVEEST CGDIPELEHG WAQLSSPPYY YGDSVEFNCS
ESFTMIGHRS ITCIHGVWTQ LPQCVAIDKL KKCKSSNLII LEEHLKNKKE FDHNSNIRYR
CRGKEGWIHT VCINGRWDPE VNCSMAQIQL CPPPPQIPNS HNMTTTLNYR DGEKVSVLCQ
ENYLIQEGEE ITCKDGRWQS IPLCVEKIPC SQPPQIEHGT INSSRSSQES YAHGTKLSYT
CEGGFRISEE NETTCYMGKW SSPPQCEGLP CKSPPEISHG VVAHMSDSYQ YGEEVTYKCF
EGFGIDGPAI AKCLGEKWSH PPSCIKTDCL SLPSFENAIP MGEKKDVYKA GEQVTYTCAT
YYKMDGASNV TCINSRWTGR PTCRDTSCVN PPTVQNAYIV SRQMSKYPSG ERVRYQCRSP
YEMFGDEEVM CLNGNWTEPP QCKDSTGKCG PPPPIDNGDI TSFPLSVYAP ASSVEYQCQN
LYQLEGNKRI TCRNGQWSEP PKCLHPCVIS REIMENYNIA LRWTAKQKLY SRTGESVEFV
CKRGYRLSSR SHTLRTTCWD GKLEYPTCAK R*
mutated AA sequence MRLLAKIICL MLWAICVAED CNELPPRRNT EILTGSWSDQ TYPEGTQAIY KCRPGYRSLG
NVIMVCRKGE WVALNPLRKC QKRPCGHPGD TPFGTFTLTG GNVFEYGVKA VYTCNEGYQL
LGEINYRECD TDGWTNDIPI CEVVKCLPVT APENGKIVSS AMEPDREYHF GQAVRFVCNS
GYKIEGDEEM HCSDDGFWSK EKPKCVEISC KSPDVINGSP ISQKIIYKEN ERFQYKCNMG
YEYSERGDAV CTESGWRPLP SCEEKSCDNP YIPNGDYSPL RIKHRTGDEI TYQCRNGFYP
ATRGNTAKCT STGWIPAPRC TLKPCDYPDI KHGGLYHENM RRPYFPVAVG KYYSYYCDEH
FETPSGSYWD HIHCTQDGWS PAVPCLRKCY FPYLENGYNQ NHGRKFVQGK SIDVACHPGY
ALPKAQTTVT CMENGWSPTP RCIRVKTCSK SSIDIENGFI SESQYTYALK EKAKYQCKLG
YVTADGETSG SITCGKDGWS AQPTCIKSCD IPVFMNARTK NDFTWFKLND TLDYECHDGY
ESNTGSTTGS IVCGYNGWSD LPICYERECE LPKIDVHLVP DRKKDQYKVG EVLKFSCKPG
FTIVGPNSVQ CYHFGLSPDL PICKEQVQSC GPPPELLNGN VKEKTKEEYG HSEVVEYYCN
PRFLMKGPNK IQCVDGEWTT LPVCIVEEST CGDIPELEHG WAQLSSPPYY YGDSVEFNCS
ESFTMIGHRS ITCIHGVWTQ LPQCVAIDKL KKCKSSNLII LEEHLKNKKE FDHNSNIRYR
CRGKEGWIHT VCINGRWDPE VNCSMAQIQL CPPPPQIPNS HNMTTTLNYR DGEKVSVLCQ
ENYLIQEGEE ITCKDGRWQS IPLCVEKIPC SQPPQIEHGT INSSRSSQES YAHGTKLSYT
CEGGFRISEE NETTCYMGKW SSPPQCEGLP CKSPPEISHG VVAHMSDSYQ YGEEVTYKCF
EGFGIDGPAI AKCLGEKWSH PPSCIKTDCL SLPSFENAIP MGEKKDVYKA GEQVTYTCAT
YYKMDGASNV TCINSRWTGR PTCRDTSCVN PPTVQNAYIV SRQMSKYPSG ERVRYQCRSP
YEMFGDEEVM CLNGNWTEPP QCKDSTGKCG PPPPIDNGDI TSFPLSVYAP ASSVEYQCQN
LYQLEGNKRI TCRNGQWSEP PKCLHPCVIS REIMENYNIA LRWTAKQKLY SRTGESAEFV
CKRGYRLSSR SHTLRTTCWD GKLEYPTCAK R*
speed 1.68 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
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Problems