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 2.749172 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CFH	disease_causing_automatic	0.0192856406092828	simple_aae		affected	0	C959Y	single base exchange	rs121913053		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.0192856406092828 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM1312934)
known disease mutation at this position (HGMD CM970725)
known disease mutation: rs16544 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:196709842G>AN/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.2876G>A
cDNA.3116G>A
g.88835G>A

AA changes

C959Y Score: 194 explain score(s)

position(s) of altered AA
if AA alteration in CDS

959

frameshift

known variant

Reference ID: rs121913053
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs16544 (pathogenic for Factor H deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970725)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1312934)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1312934)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970725)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.983	0.204
	2.162	0.202
(flanking)	-0.205	0.005

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	88837	wt: 0.35 / mu: 0.78	wt: AATGTTTTGAAGGTT mu: AATATTTTGAAGGTT	TGTT\|ttga
Donor increased	88827	wt: 0.61 / mu: 0.77	wt: GTTACGTACAAATGT mu: GTTACGTACAAATAT	TACG\|taca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

959

mutated

not conserved

959

Ptroglodytes

all identical

ENSPTRG00000001799

959

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026365

982

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000092786

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
929	986	DOMAIN	Sushi 16.	lost
957	959	STRAND		lost
959	959	DISULFID	By similarity.	lost
965	967	STRAND		might get lost (downstream of altered splice site)
971	974	STRAND		might get lost (downstream of altered splice site)
973	973	DISULFID	By similarity.	might get lost (downstream of altered splice site)
977	979	STRAND		might get lost (downstream of altered splice site)
984	984	DISULFID	By similarity.	might get lost (downstream of altered splice site)
987	1045	DOMAIN	Sushi 17.	might get lost (downstream of altered splice site)
989	989	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1018	1018	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1029	1029	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
1032	1032	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1043	1043	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1046	1104	DOMAIN	Sushi 18.	might get lost (downstream of altered splice site)
1048	1048	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1057	1059	STRAND		might get lost (downstream of altered splice site)
1065	1067	STRAND		might get lost (downstream of altered splice site)
1072	1077	STRAND		might get lost (downstream of altered splice site)
1077	1077	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1082	1085	STRAND		might get lost (downstream of altered splice site)
1087	1092	STRAND		might get lost (downstream of altered splice site)
1091	1091	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1095	1095	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
1101	1103	STRAND		might get lost (downstream of altered splice site)
1102	1102	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1107	1165	DOMAIN	Sushi 19.	might get lost (downstream of altered splice site)
1109	1109	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1118	1122	STRAND		might get lost (downstream of altered splice site)
1126	1128	STRAND		might get lost (downstream of altered splice site)
1133	1138	STRAND		might get lost (downstream of altered splice site)
1138	1138	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1143	1146	STRAND		might get lost (downstream of altered splice site)
1148	1153	STRAND		might get lost (downstream of altered splice site)
1152	1152	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1162	1164	STRAND		might get lost (downstream of altered splice site)
1163	1163	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1167	1167	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1167	1170	STRAND		might get lost (downstream of altered splice site)
1170	1230	DOMAIN	Sushi 20.	might get lost (downstream of altered splice site)
1171	1177	HELIX		might get lost (downstream of altered splice site)
1179	1181	STRAND		might get lost (downstream of altered splice site)
1182	1186	TURN		might get lost (downstream of altered splice site)
1189	1191	STRAND		might get lost (downstream of altered splice site)
1196	1201	STRAND		might get lost (downstream of altered splice site)
1201	1201	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1202	1204	TURN		might get lost (downstream of altered splice site)
1205	1207	STRAND		might get lost (downstream of altered splice site)
1214	1217	STRAND		might get lost (downstream of altered splice site)
1218	1218	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1228	1228	DISULFID	By similarity.	might get lost (downstream of altered splice site)
1228	1230	STRAND		might 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

strand

last intron/exon boundary

3734

theoretical NMD boundary in CDS

3443

length of CDS

3696

coding sequence (CDS) position

2876

cDNA position
(for ins/del: last normal base / first normal base)

3116

gDNA position
(for ins/del: last normal base / first normal base)

88835

chromosomal position
(for ins/del: last normal base / first normal base)

196709842

original gDNA sequence snippet

AGAAGAAGTTACGTACAAATGTTTTGAAGGTTTTGGAATTG

altered gDNA sequence snippet

AGAAGAAGTTACGTACAAATATTTTGAAGGTTTTGGAATTG

original cDNA sequence snippet

AGAAGAAGTTACGTACAAATGTTTTGAAGGTTTTGGAATTG

altered cDNA sequence snippet

AGAAGAAGTTACGTACAAATATTTTGAAGGTTTTGGAATTG

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 YGEEVTYKYF
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*

speed

0.63 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems