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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000339284
Querying Taster for transcript #2: ENST00000470604
Querying Taster for transcript #3: ENST00000313455
MT speed 1.58 s - this script 3.123388 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SH2D4B	polymorphism_automatic	1.5110581255029e-05	simple_aae		affected		H189R	single base exchange	rs7075840		show file
SH2D4B	polymorphism_automatic	6.05859361030303e-05	simple_aae		affected		H238R	single base exchange	rs7075840		show file
SH2D4B	polymorphism_automatic	6.05859361030303e-05	simple_aae		affected		H237R	single base exchange	rs7075840		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999984889418745 (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)

chr10:82363404A>GN/A show variant in all transcripts IGV

HGNC symbol

SH2D4B

Ensembl transcript ID

ENST00000313455

Genbank transcript ID

NM_001145719

UniProt peptide

Q5SQS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.566A>G
cDNA.644A>G
g.65747A>G

AA changes

H189R Score: 29 explain score(s)

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

189

frameshift

known variant

Reference ID: rs7075840

database	homozygous (G/G)	heterozygous	allele carriers
1000G	364	1078	1442
ExAC	4425	20218	24643

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.037	0.999
	2.941	1
(flanking)	0.424	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 increased	65738	wt: 0.21 / mu: 0.34	wt: GGACGAGTACCGACA mu: GGACGAGTACCGACG	ACGA\|gtac
Donor gained	65741	0.64	mu: CGAGTACCGACGCCA	AGTA\|ccga
Donor gained	65746	0.46	mu: ACCGACGCCACTCGC	CGAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

189

mutated

not conserved

189

Ptroglodytes

not conserved

ENSPTRG00000002687

237

Mmulatta

not conserved

ENSMMUG00000022098

237

Fcatus

not conserved

ENSFCAG00000000713

234

Mmusculus

not conserved

ENSMUSG00000037833

237

Ggallus

not conserved

ENSGALG00000002370

237

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069374

231

Dmelanogaster

no homologue

Celegans

all identical

F13B12.6

331

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
92	223	COMPBIAS	Glu-rich.	lost
325	417	DOMAIN	SH2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

930 / 930

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

310 / 310

position of stopcodon in wt / mu cDNA

1008 / 1008

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

79 / 79

chromosome

strand

last intron/exon boundary

920

theoretical NMD boundary in CDS

791

length of CDS

930

coding sequence (CDS) position

566

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

644

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

65747

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

82363404

original gDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered gDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

original cDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered cDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

wildtype AA sequence

MLPEDSGGSP DAAASDKHIQ WLLGADGEVW VWIMGEGPGD KPYEEISEEL IAERARLQAQ
REAEELWRQK EAEITKKFRD ALANEKARIL AEKWKVEMED RKAAKVLEER IHEEFKRKEE
EERKRGEEQI RLQEEQRAKE LYWTLKQAQL HCQASEKEER EWEEQLRRSK AADEERSRRA
QRARDEYRHH SLRAIQKGTV AGLSSMFREL GQSHEQEARL YHHLPDPGLP QPLALPVSRT
WERPLRPVSR DVIVRWFKEE QLPRRAGFER NTKFIAPWFH GGNYHCFRRR VTSGTLRTEG
QPTRLPSVV*

mutated AA sequence

MLPEDSGGSP DAAASDKHIQ WLLGADGEVW VWIMGEGPGD KPYEEISEEL IAERARLQAQ
REAEELWRQK EAEITKKFRD ALANEKARIL AEKWKVEMED RKAAKVLEER IHEEFKRKEE
EERKRGEEQI RLQEEQRAKE LYWTLKQAQL HCQASEKEER EWEEQLRRSK AADEERSRRA
QRARDEYRRH SLRAIQKGTV AGLSSMFREL GQSHEQEARL YHHLPDPGLP QPLALPVSRT
WERPLRPVSR DVIVRWFKEE QLPRRAGFER NTKFIAPWFH GGNYHCFRRR VTSGTLRTEG
QPTRLPSVV*

speed

0.50 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: 0.999939414063897 (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)

chr10:82363404A>GN/A show variant in all transcripts IGV

HGNC symbol

SH2D4B

Ensembl transcript ID

ENST00000339284

Genbank transcript ID

NM_207372

UniProt peptide

Q5SQS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.713A>G
cDNA.1143A>G
g.65747A>G

AA changes

H238R Score: 29 explain score(s)

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

238

frameshift

known variant

Reference ID: rs7075840

database	homozygous (G/G)	heterozygous	allele carriers
1000G	364	1078	1442
ExAC	4425	20218	24643

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.037	0.999
	2.941	1
(flanking)	0.424	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 increased	65738	wt: 0.21 / mu: 0.34	wt: GGACGAGTACCGACA mu: GGACGAGTACCGACG	ACGA\|gtac
Donor gained	65741	0.64	mu: CGAGTACCGACGCCA	AGTA\|ccga
Donor gained	65746	0.46	mu: ACCGACGCCACTCGC	CGAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

238

mutated

not conserved

238

Ptroglodytes

not conserved

ENSPTRG00000002687

237

Mmulatta

not conserved

ENSMMUG00000022098

237

Fcatus

not conserved

ENSFCAG00000000713

235

Mmusculus

not conserved

ENSMUSG00000037833

237

Ggallus

not conserved

ENSGALG00000002370

237

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069374

231

Dmelanogaster

no homologue

Celegans

all identical

F13B12.6

331

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
325	417	DOMAIN	SH2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1074 / 1074

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

358 / 358

position of stopcodon in wt / mu cDNA

1504 / 1504

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

431 / 431

chromosome

strand

last intron/exon boundary

1416

theoretical NMD boundary in CDS

935

length of CDS

1074

coding sequence (CDS) position

713

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

1143

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

65747

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

82363404

original gDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered gDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

original cDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered cDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

wildtype AA sequence

MLQQILHDMY IDPELLAELS DVQKHILFYK MREEQLRRWK ERETWEALAQ DEGLRPPKTK
RAASDKHIQW LLGADGEVWV WIMGEGPGDK PYEEISEELI AERARLQAQR EAEELWRQKE
AEITKKFRDA LANEKARILA EKWKVEMEDR KAAKVLEERI HEEFKRKEEE ERKRGEEQIR
LQEEQRAKEL YWTLKQAQLH CQASEKEERE WEEQLRRSKA ADEERSRRAQ RARDEYRHHS
LRAIQKGTVA GLSSMFRELG QSHEQEARLY HHLPDPGLPQ PLALPVRTWE RPLRPVSRDV
IVRWFKEEQL PRRAGFERNT KFIAPWFHGG NYHCFRRRVT SGTLRTEGQP TRLPSVV*

mutated AA sequence

MLQQILHDMY IDPELLAELS DVQKHILFYK MREEQLRRWK ERETWEALAQ DEGLRPPKTK
RAASDKHIQW LLGADGEVWV WIMGEGPGDK PYEEISEELI AERARLQAQR EAEELWRQKE
AEITKKFRDA LANEKARILA EKWKVEMEDR KAAKVLEERI HEEFKRKEEE ERKRGEEQIR
LQEEQRAKEL YWTLKQAQLH CQASEKEERE WEEQLRRSKA ADEERSRRAQ RARDEYRRHS
LRAIQKGTVA GLSSMFRELG QSHEQEARLY HHLPDPGLPQ PLALPVRTWE RPLRPVSRDV
IVRWFKEEQL PRRAGFERNT KFIAPWFHGG NYHCFRRRVT SGTLRTEGQP TRLPSVV*

speed

0.53 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999939414063897 (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)

chr10:82363404A>GN/A show variant in all transcripts IGV

HGNC symbol

SH2D4B

Ensembl transcript ID

ENST00000470604

Genbank transcript ID

N/A

UniProt peptide

Q5SQS7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.710A>G
cDNA.710A>G
g.65747A>G

AA changes

H237R Score: 29 explain score(s)

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

237

frameshift

known variant

Reference ID: rs7075840

database	homozygous (G/G)	heterozygous	allele carriers
1000G	364	1078	1442
ExAC	4425	20218	24643

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.037	0.999
	2.941	1
(flanking)	0.424	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 increased	65738	wt: 0.21 / mu: 0.34	wt: GGACGAGTACCGACA mu: GGACGAGTACCGACG	ACGA\|gtac
Donor gained	65741	0.64	mu: CGAGTACCGACGCCA	AGTA\|ccga
Donor gained	65746	0.46	mu: ACCGACGCCACTCGC	CGAC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

237

mutated

not conserved

237

Ptroglodytes

not conserved

ENSPTRG00000002687

237

Mmulatta

not conserved

ENSMMUG00000022098

237

Fcatus

not conserved

ENSFCAG00000000713

235

Mmusculus

not conserved

ENSMUSG00000037833

237

Ggallus

not conserved

ENSGALG00000002370

237

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000069374

231

Dmelanogaster

no homologue

Celegans

all identical

F13B12.6

331

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
325	417	DOMAIN	SH2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1296 / 1296

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

432 / 432

position of stopcodon in wt / mu cDNA

1296 / 1296

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

1 / 1

chromosome

strand

last intron/exon boundary

1204

theoretical NMD boundary in CDS

1153

length of CDS

1296

coding sequence (CDS) position

710

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

710

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

65747

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

82363404

original gDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered gDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

original cDNA sequence snippet

CGCCCGGGACGAGTACCGACACCACTCGCTCCGTGCTATCC

altered cDNA sequence snippet

CGCCCGGGACGAGTACCGACGCCACTCGCTCCGTGCTATCC

wildtype AA sequence

MLQQILHDMY IDPELLAELS DVQKHILFYK MREEQLRRWK ERETWEALAQ DEGLRPPKTK
RASDKHIQWL LGADGEVWVW IMGEGPGDKP YEEISEELIA ERARLQAQRE AEELWRQKEA
EITKKFRDAL ANEKARILAE KWKVEMEDRK AAKVLEERIH EEFKRKEEEE RKRGEEQIRL
QEEQRAKELY WTLKQAQLHC QASEKEEREW EEQLRRSKAA DEERSRRAQR ARDEYRHHSL
RAIQKGTVAG LSSMFRELGQ SHEQEARLYH HLPDPGLPQP LALPVRTWER PLRPVSRDVI
VRWFKEEQLP RRAGFERNTK FIAPWFHGII SREDAEALLE NMTEGAFLVR VSEKIWGYTL
SYRLQKGFKH FLVDASGDFY SFLGVDPNRH ATLTDLVDFH KEEIITVSGG ELLQEPCGQR
DSPPDYHLLF E*

mutated AA sequence

MLQQILHDMY IDPELLAELS DVQKHILFYK MREEQLRRWK ERETWEALAQ DEGLRPPKTK
RASDKHIQWL LGADGEVWVW IMGEGPGDKP YEEISEELIA ERARLQAQRE AEELWRQKEA
EITKKFRDAL ANEKARILAE KWKVEMEDRK AAKVLEERIH EEFKRKEEEE RKRGEEQIRL
QEEQRAKELY WTLKQAQLHC QASEKEEREW EEQLRRSKAA DEERSRRAQR ARDEYRRHSL
RAIQKGTVAG LSSMFRELGQ SHEQEARLYH HLPDPGLPQP LALPVRTWER PLRPVSRDVI
VRWFKEEQLP RRAGFERNTK FIAPWFHGII SREDAEALLE NMTEGAFLVR VSEKIWGYTL
SYRLQKGFKH FLVDASGDFY SFLGVDPNRH ATLTDLVDFH KEEIITVSGG ELLQEPCGQR
DSPPDYHLLF E*

speed

0.55 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems