MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000262093
Querying Taster for transcript #2: ENST00000382873
MT speed 0 s - this script 2.647517 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FECH	disease_causing	0.999999998570829	simple_aae		affected		C417G	single base exchange	rs146899669		show file
FECH	disease_causing	0.999999999925542	simple_aae		affected		C411G	single base exchange	rs146899669		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998570829 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM1010110)
known disease mutation at this position (HGMD CP005275)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55217985A>CN/A show variant in all transcripts IGV

HGNC symbol

FECH

Ensembl transcript ID

ENST00000382873

Genbank transcript ID

NM_001012515

UniProt peptide

P22830

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1249T>G
cDNA.1283T>G
g.36020T>G

AA changes

C417G Score: 159 explain score(s)

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

417

frameshift

known variant

Reference ID: rs146899669

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation at this position, please check HGMD for details (HGMD ID CP005275)

known disease mutation at this position, please check HGMD for details (HGMD ID CP005275)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1010110)

known disease mutation at this position, please check HGMD for details (HGMD ID CP005275)
known disease mutation at this position, please check HGMD for details (HGMD ID CM1010110)
known disease mutation at this position, please check HGMD for details (HGMD ID CP005275)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.748	1
	4.759	1
(flanking)	3.966	1

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
Acc marginally increased	36016	wt: 0.5367 / mu: 0.5496 (marginal change - not scored)	wt: TGTCCGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATC mu: TGTCCGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATC	tcct\|GTCT
Acc marginally increased	36015	wt: 0.2609 / mu: 0.3020 (marginal change - not scored)	wt: CTGTCCGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAAT mu: CTGTCCGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAAT	atcc\|TGTC
Donor gained	36019	0.31	mu: CCTGTCGGCAGGGAG	TGTC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

417

mutated

not conserved

417

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022568

417

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024588

410

Ggallus

all identical

ENSGALG00000003066

401

Trubripes

no homologue

Drerio

all identical

ENSDARG00000003462

397

Dmelanogaster

all identical

FBgn0024891

371

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020888

405

protein features

start (aa)	end (aa)	feature	details
410	419	HELIX		lost
417	417	MUTAGEN	F->L: Decreased activity.	lost
417	417	MUTAGEN	F->Y,W: Greatly reduced activity.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1290 / 1290

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

430 / 430

position of stopcodon in wt / mu cDNA

1324 / 1324

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

35 / 35

chromosome

strand

-1

last intron/exon boundary

1190

theoretical NMD boundary in CDS

1105

length of CDS

1290

coding sequence (CDS) position

1249

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

1283

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

36020

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

55217985

original gDNA sequence snippet

CGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATCCTTC

altered gDNA sequence snippet

CGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATCCTTC

original cDNA sequence snippet

CGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATCCTTC

altered cDNA sequence snippet

CGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATCCTTC

wildtype AA sequence

MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRYESNI RKPKTGILML NMGGPETLGD VHDFLLRLFL DRDLMTLPIQ NKLAPFIAKR
RTPKIQEQYR RIGGGSPIKI WTSKQGEGMV KLLDELSPNT APHKYYIGFR YVHPLTEEAI
EEMERDGLER AIAFTQYPQY SCSTTGSSLN AIYRYYNQVG RKPTMKWSTI DRWPTHHLLI
QCFADHILKE LDHFPLEKRS EVVILFSAHS LPMSVVNRGD PYPQEVSATV QKVMERLEYC
NPYRLVWQSK VGPMPWLGPQ TDESIKGLCE RGRKNILLVP IAFTSDHIET LYELDIEYSQ
VLAKECGVEN IRRAESLNGN PLFSKALADL VHSHIQSNEL CSKQLTLSCP LCVNPVCRET
KSFFTSQQL*

mutated AA sequence

speed

0.32 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999925542 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM1010110)
known disease mutation at this position (HGMD CP005275)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr18:55217985A>CN/A show variant in all transcripts IGV

HGNC symbol

FECH

Ensembl transcript ID

ENST00000262093

Genbank transcript ID

NM_000140

UniProt peptide

P22830

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1231T>G
cDNA.1383T>G
g.36020T>G

AA changes

C411G Score: 159 explain score(s)

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

411

frameshift

known variant

Reference ID: rs146899669

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.748	1
	4.759	1
(flanking)	3.966	1

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
Acc marginally increased	36016	wt: 0.5367 / mu: 0.5496 (marginal change - not scored)	wt: TGTCCGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATC mu: TGTCCGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATC	tcct\|GTCT
Acc marginally increased	36015	wt: 0.2609 / mu: 0.3020 (marginal change - not scored)	wt: CTGTCCGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAAT mu: CTGTCCGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAAT	atcc\|TGTC
Donor gained	36019	0.31	mu: CCTGTCGGCAGGGAG	TGTC\|ggca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

411

mutated

not conserved

411

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000022568

417

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000024588

410

Ggallus

all identical

ENSGALG00000003066

401

Trubripes

no homologue

Drerio

all identical

ENSDARG00000003462

397

Dmelanogaster

all identical

FBgn0024891

371

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020888

405

protein features

start (aa)	end (aa)	feature	details
410	419	HELIX		lost
411	411	METAL	Iron-sulfur (2Fe-2S).	lost
411	411	MUTAGEN	C->H,S: Loss of activity.	lost
417	417	MUTAGEN	F->L: Decreased activity.	might get lost (downstream of altered splice site)
417	417	MUTAGEN	F->Y,W: Greatly reduced activity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1272 / 1272

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

424 / 424

position of stopcodon in wt / mu cDNA

1424 / 1424

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

153 / 153

chromosome

strand

-1

last intron/exon boundary

1290

theoretical NMD boundary in CDS

1087

length of CDS

1272

coding sequence (CDS) position

1231

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

1383

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

36020

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

55217985

original gDNA sequence snippet

CGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATCCTTC

altered gDNA sequence snippet

CGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATCCTTC

original cDNA sequence snippet

CGCTCTGTGTCAATCCTGTCTGCAGGGAGACTAAATCCTTC

altered cDNA sequence snippet

CGCTCTGTGTCAATCCTGTCGGCAGGGAGACTAAATCCTTC

wildtype AA sequence

MRSLGANMAA ALRAAGVLLR DPLASSSWRV CQPWRWKSGA AAAAVTTETA QHAQGAKPQV
QPQKRKPKTG ILMLNMGGPE TLGDVHDFLL RLFLDRDLMT LPIQNKLAPF IAKRRTPKIQ
EQYRRIGGGS PIKIWTSKQG EGMVKLLDEL SPNTAPHKYY IGFRYVHPLT EEAIEEMERD
GLERAIAFTQ YPQYSCSTTG SSLNAIYRYY NQVGRKPTMK WSTIDRWPTH HLLIQCFADH
ILKELDHFPL EKRSEVVILF SAHSLPMSVV NRGDPYPQEV SATVQKVMER LEYCNPYRLV
WQSKVGPMPW LGPQTDESIK GLCERGRKNI LLVPIAFTSD HIETLYELDI EYSQVLAKEC
GVENIRRAES LNGNPLFSKA LADLVHSHIQ SNELCSKQLT LSCPLCVNPV CRETKSFFTS
QQL*

mutated AA sequence

speed

0.33 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems