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: ENST00000405876
Querying Taster for transcript #2: ENST00000312777
MT speed 0 s - this script 2.644616 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TCHP	polymorphism_automatic	4.44258667060549e-05	simple_aae				K127R	single base exchange	rs10774978		show file
TCHP	polymorphism_automatic	4.44258667060549e-05	simple_aae				K127R	single base exchange	rs10774978		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999955574133294 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110341933A>GN/A show variant in all transcripts IGV

HGNC symbol

TCHP

Ensembl transcript ID

ENST00000405876

Genbank transcript ID

NM_001143852

UniProt peptide

Q9BT92

alteration type

single base exchange

alteration region

CDS

DNA changes

c.380A>G
cDNA.527A>G
g.3865A>G

AA changes

K127R Score: 26 explain score(s)

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

127

frameshift

known variant

Reference ID: rs10774978

database	homozygous (G/G)	heterozygous	allele carriers
1000G	380	802	1182
ExAC	1549	7681	9230

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.385	0.984
	1.738	0.998
(flanking)	0.657	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
Donor marginally increased	3864	wt: 0.9914 / mu: 0.9986 (marginal change - not scored)	wt: CAGCCAAAGAAGAGC mu: CAGCCAGAGAAGAGC	GCCA\|aaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

127

mutated

all conserved

127

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000011503

129

Mmusculus

all conserved

ENSMUSG00000002486

126

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000014974

128

Drerio

all conserved

ENSDARG00000035605

128

Dmelanogaster

all identical

FBgn0036242

165

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000018633

128

protein features

start (aa)	end (aa)	feature	details
66	136	COILED	Potential.	lost
70	482	COMPBIAS	Glu-rich.	lost
73	498	REGION	Interaction with keratin proteins.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

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

499 / 499

position of stopcodon in wt / mu cDNA

1644 / 1644

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

148 / 148

chromosome

strand

last intron/exon boundary

1612

theoretical NMD boundary in CDS

1414

length of CDS

1497

coding sequence (CDS) position

380

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

527

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

3865

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

110341933

original gDNA sequence snippet

CGGGAAGCTGAAATCAGCCAAAGAAGAGCAGAGGAAACTGG

altered gDNA sequence snippet

CGGGAAGCTGAAATCAGCCAGAGAAGAGCAGAGGAAACTGG

original cDNA sequence snippet

CGGGAAGCTGAAATCAGCCAAAGAAGAGCAGAGGAAACTGA

altered cDNA sequence snippet

CGGGAAGCTGAAATCAGCCAGAGAAGAGCAGAGGAAACTGA

wildtype AA sequence

MALPTLPSYW CSQQRLNQQL ARQREQEARL RQQWEQNSRY FRMSDICSSK QAEWSSKTSY
QRSMHAYQRE KMKEEKRRSL EARREKLRQL MQEEQDLLAR ELEELRLSMN LQERRIREQH
GKLKSAKEEQ RKLIAEQLLY EHWKKNNPKL REMELDLHQK HVVNSWEMQK EEKKQQEATA
EQENKRYENE YERARREALE RMKAEEERRQ LEDKLQAEAL LQQMEELKLK EVEATKLKKE
QENLLKQRWE LERLEEERKQ MEAFRQKAEL GRFLRHQYNA QLSRRTQQIQ EELEADRRIL
QALLEKEDES QRLHLARREQ VMADVAWMKQ AIEEQLQLER AREAELQMLL REEAKEMWEK
REAEWARERS ARDRLMSEVL TGRQQQIQEK IEQNRRAQEE SLKHREQLIR NLEEVRELAR
REKEESEKLK SARKQELEAQ VAERRLQAWE ADQQEEEEEE EARRVEQLSD ALLQQEAETM
AEQGYRPKPY GHPKIAWN*

mutated AA sequence

MALPTLPSYW CSQQRLNQQL ARQREQEARL RQQWEQNSRY FRMSDICSSK QAEWSSKTSY
QRSMHAYQRE KMKEEKRRSL EARREKLRQL MQEEQDLLAR ELEELRLSMN LQERRIREQH
GKLKSAREEQ RKLIAEQLLY EHWKKNNPKL REMELDLHQK HVVNSWEMQK EEKKQQEATA
EQENKRYENE YERARREALE RMKAEEERRQ LEDKLQAEAL LQQMEELKLK EVEATKLKKE
QENLLKQRWE LERLEEERKQ MEAFRQKAEL GRFLRHQYNA QLSRRTQQIQ EELEADRRIL
QALLEKEDES QRLHLARREQ VMADVAWMKQ AIEEQLQLER AREAELQMLL REEAKEMWEK
REAEWARERS ARDRLMSEVL TGRQQQIQEK IEQNRRAQEE SLKHREQLIR NLEEVRELAR
REKEESEKLK SARKQELEAQ VAERRLQAWE ADQQEEEEEE EARRVEQLSD ALLQQEAETM
AEQGYRPKPY GHPKIAWN*

speed

0.30 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

polymorphism

Model: simple_aae, prob: 0.999955574133294 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:110341933A>GN/A show variant in all transcripts IGV

HGNC symbol

TCHP

Ensembl transcript ID

ENST00000312777

Genbank transcript ID

NM_032300

UniProt peptide

Q9BT92

alteration type

single base exchange

alteration region

CDS

DNA changes

c.380A>G
cDNA.594A>G
g.3865A>G

AA changes

K127R Score: 26 explain score(s)

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

127

frameshift

known variant

Reference ID: rs10774978

database	homozygous (G/G)	heterozygous	allele carriers
1000G	380	802	1182
ExAC	1549	7681	9230

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.385	0.984
	1.738	0.998
(flanking)	0.657	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
Donor marginally increased	3864	wt: 0.9914 / mu: 0.9986 (marginal change - not scored)	wt: CAGCCAAAGAAGAGC mu: CAGCCAGAGAAGAGC	GCCA\|aaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

127

mutated

all conserved

127

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

all conserved

ENSFCAG00000011503

129

Mmusculus

all conserved

ENSMUSG00000002486

126

Ggallus

no homologue

Trubripes

all conserved

ENSTRUG00000014974

128

Drerio

all conserved

ENSDARG00000035605

128

Dmelanogaster

all identical

FBgn0036242

165

Celegans

no homologue

Xtropicalis

all conserved

ENSXETG00000018633

128

protein features

start (aa)	end (aa)	feature	details
66	136	COILED	Potential.	lost
70	482	COMPBIAS	Glu-rich.	lost
73	498	REGION	Interaction with keratin proteins.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1497 / 1497

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

499 / 499

position of stopcodon in wt / mu cDNA

1711 / 1711

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

215 / 215

chromosome

strand

last intron/exon boundary

1679

theoretical NMD boundary in CDS

1414

length of CDS

1497

coding sequence (CDS) position

380

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

594

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

3865

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

110341933

original gDNA sequence snippet

CGGGAAGCTGAAATCAGCCAAAGAAGAGCAGAGGAAACTGG

altered gDNA sequence snippet

CGGGAAGCTGAAATCAGCCAGAGAAGAGCAGAGGAAACTGG

original cDNA sequence snippet

CGGGAAGCTGAAATCAGCCAAAGAAGAGCAGAGGAAACTGA

altered cDNA sequence snippet

CGGGAAGCTGAAATCAGCCAGAGAAGAGCAGAGGAAACTGA

wildtype AA sequence

mutated AA sequence

speed

0.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems