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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000564763
Querying Taster for transcript #2: ENST00000381605
Querying Taster for transcript #3: ENST00000381603
Querying Taster for transcript #4: ENST00000262929
MT speed 0 s - this script 3.700817 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SIRPB1	polymorphism_automatic	3.19744231092045e-14	simple_aae		affected		A146P	single base exchange	rs2243603		show file
SIRPB1	polymorphism_automatic	3.19744231092045e-14	simple_aae		affected		A363P	single base exchange	rs2243603		show file
SIRPB1	polymorphism_automatic	3.19744231092045e-14	simple_aae		affected		A145P	single base exchange	rs2243603		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999968 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM168234)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:1546911C>GN/A show variant in all transcripts IGV

HGNC symbol

SIRPB1

Ensembl transcript ID

ENST00000381603

Genbank transcript ID

NM_001083910

UniProt peptide

O00241

alteration type

single base exchange

alteration region

CDS

DNA changes

c.436G>C
cDNA.488G>C
g.53797G>C

AA changes

A146P Score: 27 explain score(s)

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

146

frameshift

known variant

Reference ID: rs2243603

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1658	731	2389
ExAC	28014	-23261	4753

known disease mutation at this position, please check HGMD for details (HGMD ID CM168234)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.628	0
	-0.952	0
(flanking)	-1.922	0

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	53794.5	sequence motif lost	-	wt: tcca\|GAAG mu: tcca.GAAC
Acc marginally increased	53794	wt: 0.8380 / mu: 0.8827 (marginal change - not scored)	wt: CTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACT mu: CTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACT	ccag\|AAGC
Acc marginally increased	53791	wt: 0.4545 / mu: 0.5182 (marginal change - not scored)	wt: CTCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCT mu: CTCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCT	tttc\|CAGA
Acc marginally increased	53792	wt: 0.6986 / mu: 0.7055 (marginal change - not scored)	wt: TCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTA mu: TCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTA	ttcc\|AGAA
Donor increased	53799	wt: 0.31 / mu: 0.57	wt: GAAGCAGCGCTGGCT mu: GAACCAGCGCTGGCT	AGCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

146

mutated

not conserved

146

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000018474

146

Fcatus

not conserved

ENSFCAG00000003555

147

Mmusculus

not conserved

ENSMUSG00000037902

Ggallus

not conserved

ENSGALG00000006176

141

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	371	TOPO_DOM	Extracellular (Potential).	lost
147	246	DOMAIN	Ig-like C1-type 1.	might get lost (downstream of altered splice site)
169	169	DISULFID	Potential.	might get lost (downstream of altered splice site)
227	227	DISULFID	Potential.	might get lost (downstream of altered splice site)
244	244	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
253	347	DOMAIN	Ig-like C1-type 2.	might get lost (downstream of altered splice site)
269	269	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
291	291	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
320	320	DISULFID	Interchain.	might get lost (downstream of altered splice site)
320	320	DISULFID	Interchain.	might get lost (downstream of altered splice site)
372	392	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
393	398	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

546 / 546

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

182 / 182

position of stopcodon in wt / mu cDNA

598 / 598

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

53 / 53

chromosome

strand

-1

last intron/exon boundary

601

theoretical NMD boundary in CDS

498

length of CDS

546

coding sequence (CDS) position

436

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

488

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

53797

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

1546911

original gDNA sequence snippet

CTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACTGCT

altered gDNA sequence snippet

CTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACTGCT

original cDNA sequence snippet

CTGAGCTGTCTGTGCGCGAAGCAGCGCTGGCTCCTACTGCT

altered cDNA sequence snippet

CTGAGCTGTCTGTGCGCGAACCAGCGCTGGCTCCTACTGCT

wildtype AA sequence

MPVPASWPHL PSPFLLMTLL LGRLTGVAGE DELQVIQPEK SVSVAAGESA TLRCAMTSLI
PVGPIMWFRG AGAGRELIYN QKEGHFPRVT TVSELTKRNN LDFSISISNI TPADAGTYYC
VKFRKGSPDD VEFKSGAGTE LSVREAALAP TAPLLVALLL GPKLLLVVGV SAIYICWKQK
A*

mutated AA sequence

MPVPASWPHL PSPFLLMTLL LGRLTGVAGE DELQVIQPEK SVSVAAGESA TLRCAMTSLI
PVGPIMWFRG AGAGRELIYN QKEGHFPRVT TVSELTKRNN LDFSISISNI TPADAGTYYC
VKFRKGSPDD VEFKSGAGTE LSVREPALAP TAPLLVALLL GPKLLLVVGV SAIYICWKQK
A*

speed

0.93 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: 0.999999999999968 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM168234)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:1546911C>GN/A show variant in all transcripts IGV

HGNC symbol

SIRPB1

Ensembl transcript ID

ENST00000381605

Genbank transcript ID

NM_006065

UniProt peptide

O00241

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1087G>C
cDNA.1152G>C
g.53797G>C

AA changes

A363P Score: 27 explain score(s)

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

363

frameshift

known variant

Reference ID: rs2243603

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1658	731	2389
ExAC	28014	-23261	4753

known disease mutation at this position, please check HGMD for details (HGMD ID CM168234)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.628	0
	-0.952	0
(flanking)	-1.922	0

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	53794.5	sequence motif lost	-	wt: tcca\|GAAG mu: tcca.GAAC
Acc marginally increased	53794	wt: 0.8380 / mu: 0.8827 (marginal change - not scored)	wt: CTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACT mu: CTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACT	ccag\|AAGC
Acc marginally increased	53791	wt: 0.4545 / mu: 0.5182 (marginal change - not scored)	wt: CTCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCT mu: CTCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCT	tttc\|CAGA
Acc marginally increased	53792	wt: 0.6986 / mu: 0.7055 (marginal change - not scored)	wt: TCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTA mu: TCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTA	ttcc\|AGAA
Donor increased	53799	wt: 0.31 / mu: 0.57	wt: GAAGCAGCGCTGGCT mu: GAACCAGCGCTGGCT	AGCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

363

mutated

not conserved

363

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000018474

362

Fcatus

not conserved

ENSFCAG00000003555

364

Mmusculus

not conserved

ENSMUSG00000037902

373

NVF

Ggallus

not conserved

ENSGALG00000006176

360

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	371	TOPO_DOM	Extracellular (Potential).	lost
372	392	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
393	398	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1197 / 1197

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

399 / 399

position of stopcodon in wt / mu cDNA

1262 / 1262

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

66 / 66

chromosome

strand

-1

last intron/exon boundary

1265

theoretical NMD boundary in CDS

1149

length of CDS

1197

coding sequence (CDS) position

1087

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

1152

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

53797

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

1546911

original gDNA sequence snippet

CTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACTGCT

altered gDNA sequence snippet

CTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACTGCT

original cDNA sequence snippet

GCTCAGATATCACCCATGAAGCAGCGCTGGCTCCTACTGCT

altered cDNA sequence snippet

GCTCAGATATCACCCATGAACCAGCGCTGGCTCCTACTGCT

wildtype AA sequence

MPVPASWPHL PSPFLLMTLL LGRLTGVAGE DELQVIQPEK SVSVAAGESA TLRCAMTSLI
PVGPIMWFRG AGAGRELIYN QKEGHFPRVT TVSELTKRNN LDFSISISNI TPADAGTYYC
VKFRKGSPDD VEFKSGAGTE LSVRAKPSAP VVSGPAVRAT PEHTVSFTCE SHGFSPRDIT
LKWFKNGNEL SDFQTNVDPA GDSVSYSIHS TARVVLTRGD VHSQVICEIA HITLQGDPLR
GTANLSEAIR VPPTLEVTQQ PMRAENQANV TCQVSNFYPR GLQLTWLENG NVSRTETAST
LIENKDGTYN WMSWLLVNTC AHRDDVVLTC QVEHDGQQAV SKSYALEISA HQKEHGSDIT
HEAALAPTAP LLVALLLGPK LLLVVGVSAI YICWKQKA*

mutated AA sequence

speed

0.68 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999968 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM168234)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:1546911C>GN/A show variant in all transcripts IGV

HGNC symbol

SIRPB1

Ensembl transcript ID

ENST00000262929

Genbank transcript ID

N/A

UniProt peptide

O00241

alteration type

single base exchange

alteration region

CDS

DNA changes

c.433G>C
cDNA.433G>C
g.53797G>C

AA changes

A145P Score: 27 explain score(s)

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

145

frameshift

known variant

Reference ID: rs2243603

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1658	731	2389
ExAC	28014	-23261	4753

known disease mutation at this position, please check HGMD for details (HGMD ID CM168234)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.628	0
	-0.952	0
(flanking)	-1.922	0

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Acceptor lost	53794.5	sequence motif lost	-	wt: tcca\|GAAG mu: tcca.GAAC
Acc marginally increased	53794	wt: 0.8380 / mu: 0.8827 (marginal change - not scored)	wt: CTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACT mu: CTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACT	ccag\|AAGC
Acc marginally increased	53791	wt: 0.4545 / mu: 0.5182 (marginal change - not scored)	wt: CTCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCT mu: CTCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCT	tttc\|CAGA
Acc marginally increased	53792	wt: 0.6986 / mu: 0.7055 (marginal change - not scored)	wt: TCCTCCTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTA mu: TCCTCCTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTA	ttcc\|AGAA
Donor increased	53799	wt: 0.31 / mu: 0.57	wt: GAAGCAGCGCTGGCT mu: GAACCAGCGCTGGCT	AGCA\|gcgc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

145

mutated

not conserved

145

Ptroglodytes

no homologue

Mmulatta

not conserved

ENSMMUG00000018474

146

Fcatus

not conserved

ENSFCAG00000003555

148

Mmusculus

not conserved

ENSMUSG00000037902

Ggallus

not conserved

ENSGALG00000006176

141

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	371	TOPO_DOM	Extracellular (Potential).	lost
147	246	DOMAIN	Ig-like C1-type 1.	might get lost (downstream of altered splice site)
169	169	DISULFID	Potential.	might get lost (downstream of altered splice site)
227	227	DISULFID	Potential.	might get lost (downstream of altered splice site)
244	244	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
253	347	DOMAIN	Ig-like C1-type 2.	might get lost (downstream of altered splice site)
269	269	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
291	291	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
320	320	DISULFID	Interchain.	might get lost (downstream of altered splice site)
320	320	DISULFID	Interchain.	might get lost (downstream of altered splice site)
372	392	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
393	398	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

543 / 543

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

181 / 181

position of stopcodon in wt / mu cDNA

543 / 543

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

-1

last intron/exon boundary

546

theoretical NMD boundary in CDS

495

length of CDS

543

coding sequence (CDS) position

433

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

433

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

53797

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

1546911

original gDNA sequence snippet

CTCTTCCCTGATTTCCAGAAGCAGCGCTGGCTCCTACTGCT

altered gDNA sequence snippet

CTCTTCCCTGATTTCCAGAACCAGCGCTGGCTCCTACTGCT

original cDNA sequence snippet

CTGAGCTGTCTGTGCGCGAAGCAGCGCTGGCTCCTACTGCT

altered cDNA sequence snippet

CTGAGCTGTCTGTGCGCGAACCAGCGCTGGCTCCTACTGCT

wildtype AA sequence

MPVPASWPHP PCPFLLLTLL LGLTGVAGED ELQVIQPEKS VSVAAGESAT LRCAMTSLIP
VGPIMWFRGA GAGRELIYNQ KEGHFPRVTT VSELTKRNNL DFSISISNIT PADAGTYYCV
KFRKGSPDDV EFKSGAGTEL SVREAALAPT APLLVALLLG PKLLLVVGVS AIYICWKQKA
*

mutated AA sequence

MPVPASWPHP PCPFLLLTLL LGLTGVAGED ELQVIQPEKS VSVAAGESAT LRCAMTSLIP
VGPIMWFRGA GAGRELIYNQ KEGHFPRVTT VSELTKRNNL DFSISISNIT PADAGTYYCV
KFRKGSPDDV EFKSGAGTEL SVREPALAPT APLLVALLLG PKLLLVVGVS AIYICWKQKA
*

speed

0.67 s

Problems

data problem

No NCBI gene ID found for this transcript

back to results table