MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000298466
Querying Taster for transcript #2: ENST00000425225
MT speed 0 s - this script 4.217076 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SOHLH1	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R37Q	single base exchange	rs471525		show file
SOHLH1	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		R37Q	single base exchange	rs471525		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:138590928C>TN/A show variant in all transcripts IGV

HGNC symbol

SOHLH1

Ensembl transcript ID

ENST00000298466

Genbank transcript ID

NM_001012415

UniProt peptide

Q5JUK2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110G>A
cDNA.171G>A
g.447G>A

AA changes

R37Q Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs471525

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1668	711	2379
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.548	0.01
	-1.49	0
(flanking)	2.076	0.003

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 gained	442	0.64	mu: GACTCGGCCCAGGGC	CTCG\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000021540

Mmulatta

all conserved

ENSMMUG00000021495

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000059625

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
53	104	DOMAIN	bHLH.	might get lost (downstream of altered splice site)
293	293	CONFLICT	S -> F (in Ref. 6; DB304976).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

987 / 987

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

329 / 329

position of stopcodon in wt / mu cDNA

1048 / 1048

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

62 / 62

chromosome

strand

-1

last intron/exon boundary

937

theoretical NMD boundary in CDS

825

length of CDS

987

coding sequence (CDS) position

110

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

171

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

447

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

138590928

original gDNA sequence snippet

CTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGG

altered gDNA sequence snippet

CTGCTGCGAGGACTCGGCCCAGGGCTCGGGCCCGCCCAAGG

original cDNA sequence snippet

CTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGG

altered cDNA sequence snippet

CTGCTGCGAGGACTCGGCCCAGGGCTCGGGCCCGCCCAAGG

wildtype AA sequence

MASRCSEPYP EVSRIPTVRG CNGSLSGALS CCEDSARGSG PPKAPTVAEG PSSCLRRNVI
SERERRKRMS LSCERLRALL PQFDGRREDM ASVLEMSVQF LRLASALGPS QEQHAILASS
KEMWHSLQED VLQLTLSSQI QAGVPDPGTG ASSGTRTPDV KAFLESPWSL DPASASPEPV
PHILASSRQW DPASCTSLGT DKCEALLGLC QVRGGLPPFS EPSSLVPWPP GRSLPKAVRP
PLSWPPFSQQ QTLPVMSGEA LGWLGQAGPL AMGAAPLGEP AKEDPMLAQE AGSALGSDVD
DGTSFLLTAG PSSWPGEWGP GFRAGPPA*

mutated AA sequence

MASRCSEPYP EVSRIPTVRG CNGSLSGALS CCEDSAQGSG PPKAPTVAEG PSSCLRRNVI
SERERRKRMS LSCERLRALL PQFDGRREDM ASVLEMSVQF LRLASALGPS QEQHAILASS
KEMWHSLQED VLQLTLSSQI QAGVPDPGTG ASSGTRTPDV KAFLESPWSL DPASASPEPV
PHILASSRQW DPASCTSLGT DKCEALLGLC QVRGGLPPFS EPSSLVPWPP GRSLPKAVRP
PLSWPPFSQQ QTLPVMSGEA LGWLGQAGPL AMGAAPLGEP AKEDPMLAQE AGSALGSDVD
DGTSFLLTAG PSSWPGEWGP GFRAGPPA*

speed

1.24 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: 0.999999999999995 (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
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr9:138590928C>TN/A show variant in all transcripts IGV

HGNC symbol

SOHLH1

Ensembl transcript ID

ENST00000425225

Genbank transcript ID

NM_001101677

UniProt peptide

Q5JUK2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110G>A
cDNA.171G>A
g.447G>A

AA changes

R37Q Score: 43 explain score(s)

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

frameshift

known variant

Reference ID: rs471525

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1668	711	2379
ExAC	-	-	-

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.548	0.01
	-1.49	0
(flanking)	2.076	0.003

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 gained	442	0.64	mu: GACTCGGCCCAGGGC	CTCG\|gccc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all conserved

ENSPTRG00000021540

Mmulatta

all conserved

ENSMMUG00000021495

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000059625

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
53	104	DOMAIN	bHLH.	might get lost (downstream of altered splice site)
293	293	CONFLICT	S -> F (in Ref. 6; DB304976).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1164 / 1164

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

388 / 388

position of stopcodon in wt / mu cDNA

1225 / 1225

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

62 / 62

chromosome

strand

-1

last intron/exon boundary

1008

theoretical NMD boundary in CDS

896

length of CDS

1164

coding sequence (CDS) position

110

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

171

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

447

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

138590928

original gDNA sequence snippet

CTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGG

altered gDNA sequence snippet

CTGCTGCGAGGACTCGGCCCAGGGCTCGGGCCCGCCCAAGG

original cDNA sequence snippet

CTGCTGCGAGGACTCGGCCCGGGGCTCGGGCCCGCCCAAGG

altered cDNA sequence snippet

CTGCTGCGAGGACTCGGCCCAGGGCTCGGGCCCGCCCAAGG

wildtype AA sequence

mutated AA sequence

speed

0.98 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems