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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 4.167297 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CFHdisease_causing_automatic8.36201585047839e-12simple_aaeaffected0R1210Csingle base exchangers121913059show file

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documentation

Prediction

disease causing

Model: simple_aae, prob: 8.36201585047839e-12 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010323)
  • known disease mutation: rs16558 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:196716375C>TN/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.3628C>T
cDNA.3868C>T
g.95368C>T
AA changes R1210C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS
1210
frameshift no
known variant Reference ID: rs121913059
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC02121

known disease mutation: rs16558 (pathogenic for Basal laminar drusen|Atypical hemolytic-uremic syndrome 1|Factor H deficiency|Age-related macular degeneration 4|Atypical hemolytic uremic syndrome|CFH-Related Dense Deposit Disease / Membranoproliferative Glomerulonephritis Type II) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010323)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010323)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010323)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2860
-3.330
(flanking)-2.1140
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased95367wt: 0.7824 / mu: 0.8086 (marginal change - not scored)wt: CGGGGATATCGTCTTTCATCACGTTCTCACACATTGCGAAC
mu: CGGGGATATCGTCTTTCATCATGTTCTCACACATTGCGAAC
 atca|CGTT
Acc marginally increased95375wt: 0.4037 / mu: 0.4437 (marginal change - not scored)wt: TCGTCTTTCATCACGTTCTCACACATTGCGAACAACATGTT
mu: TCGTCTTTCATCATGTTCTCACACATTGCGAACAACATGTT
 ctca|CACA
Acc marginally increased95378wt: 0.9361 / mu: 0.9651 (marginal change - not scored)wt: TCTTTCATCACGTTCTCACACATTGCGAACAACATGTTGGG
mu: TCTTTCATCATGTTCTCACACATTGCGAACAACATGTTGGG
 acac|ATTG
Acc increased95376wt: 0.52 / mu: 0.58wt: CGTCTTTCATCACGTTCTCACACATTGCGAACAACATGTTG
mu: CGTCTTTCATCATGTTCTCACACATTGCGAACAACATGTTG
 tcac|ACAT
Acc marginally increased95370wt: 0.9386 / mu: 0.9629 (marginal change - not scored)wt: GGATATCGTCTTTCATCACGTTCTCACACATTGCGAACAAC
mu: GGATATCGTCTTTCATCATGTTCTCACACATTGCGAACAAC
 acgt|TCTC
Acc increased95374wt: 0.69 / mu: 0.77wt: ATCGTCTTTCATCACGTTCTCACACATTGCGAACAACATGT
mu: ATCGTCTTTCATCATGTTCTCACACATTGCGAACAACATGT
 tctc|ACAC
distance from splice site 135
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1210FVCKRGYRLSSRSHTLRTTCWDGK
mutated  not conserved    1210CKRGYRLSSCSHTLRTTCWDG
Ptroglodytes  not conserved  ENSPTRG00000001799  1210CKNGYRLSPSSHALRTACWDG
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000026365  1233FGCKYGYYKARDSPPFRTKCING
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000092786  350FACLRENERMKGNS---KQICNDG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
11701230DOMAINSushi 20.lost
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 3628
cDNA position
(for ins/del: last normal base / first normal base)
3868
gDNA position
(for ins/del: last normal base / first normal base)
95368
chromosomal position
(for ins/del: last normal base / first normal base)
196716375
original gDNA sequence snippet GGGGATATCGTCTTTCATCACGTTCTCACACATTGCGAACA
altered gDNA sequence snippet GGGGATATCGTCTTTCATCATGTTCTCACACATTGCGAACA
original cDNA sequence snippet GGGGATATCGTCTTTCATCACGTTCTCACACATTGCGAACA
altered cDNA sequence snippet GGGGATATCGTCTTTCATCATGTTCTCACACATTGCGAACA
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 SRTGESVEFV
CKRGYRLSSC SHTLRTTCWD GKLEYPTCAK R*
speed 1.80 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