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: ENST00000259216
MT speed 0 s - this script 2.953136 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CFC1	disease_causing_automatic	0.999997672088315	simple_aae			0	R112C	single base exchange	rs104893611		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999997672088315 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002874)
known disease mutation: rs5187 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:131355469G>AN/A show variant in all transcripts IGV

HGNC symbol

CFC1

Ensembl transcript ID

ENST00000259216

Genbank transcript ID

NM_032545

UniProt peptide

P0CG36

alteration type

single base exchange

alteration region

CDS

DNA changes

c.334C>T
cDNA.597C>T
g.1655C>T

AA changes

R112C Score: 180 explain score(s)

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

112

frameshift

known variant

Reference ID: rs104893611
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5187 (pathogenic for Heterotaxy, visceral, 2, autosomal) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002874)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002874)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002874)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.478	1
	0.917	1
(flanking)	0.434	1

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

112

mutated

not conserved

112

Ptroglodytes

all identical

ENSPTRG00000012455

112

Mmulatta

all identical

ENSMMUG00000021625

112

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000026124

120

Ggallus

all identical

ENSGALG00000012623

113

Trubripes

no homologue

Drerio

all identical

ENSDARG00000035095

106

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000033585

protein features

start (aa)	end (aa)	feature	details
86	115	DOMAIN	EGF-like.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

672 / 672

position (AA) of stopcodon in wt / mu AA sequence

224 / 224

position of stopcodon in wt / mu cDNA

935 / 935

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

264 / 264

chromosome

strand

-1

last intron/exon boundary

736

theoretical NMD boundary in CDS

422

length of CDS

672

coding sequence (CDS) position

334

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

597

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

1655

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

131355469

original gDNA sequence snippet

GCCCGGCCCACTTCACCGGCCGCTACTGCGAGCATGACCAG

altered gDNA sequence snippet

GCCCGGCCCACTTCACCGGCTGCTACTGCGAGCATGACCAG

original cDNA sequence snippet

GCCCGGCCCACTTCACCGGCCGCTACTGCGAGCATGACCAG

altered cDNA sequence snippet

GCCCGGCCCACTTCACCGGCTGCTACTGCGAGCATGACCAG

wildtype AA sequence

MTWRHHVRLL FTVSLALQII NLGNSYQREK HNGGREEVTK VATQKHRQSP LNWTSSHFGE
VTGSAEGWGP EEPLPYSRAF GEGASARPRC CRNGGTCVLG SFCVCPAHFT GRYCEHDQRR
SECGALEHGA WTLRACHLCR CIFGALHCLP LQTPDRCDPK DFLASHAHGP SAGGAPSLLL
LLPCALLHRL LRPDAPAHPR SLVPSVLQRE RRPCGRPGLG HRL*

mutated AA sequence

MTWRHHVRLL FTVSLALQII NLGNSYQREK HNGGREEVTK VATQKHRQSP LNWTSSHFGE
VTGSAEGWGP EEPLPYSRAF GEGASARPRC CRNGGTCVLG SFCVCPAHFT GCYCEHDQRR
SECGALEHGA WTLRACHLCR CIFGALHCLP LQTPDRCDPK DFLASHAHGP SAGGAPSLLL
LLPCALLHRL LRPDAPAHPR SLVPSVLQRE RRPCGRPGLG HRL*

speed

0.89 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