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: ENST00000198536
Querying Taster for transcript #2: ENST00000453419
Querying Taster for transcript #3: ENST00000394000
Querying Taster for transcript #4: ENST00000350573
MT speed 0 s - this script 5.442227 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PILRA	polymorphism_automatic	2.4004020993118e-11	simple_aae		affected		R78G	single base exchange	rs1859788		show file
PILRA	polymorphism_automatic	2.4004020993118e-11	simple_aae		affected		R78G	single base exchange	rs1859788		show file
PILRA	polymorphism_automatic	2.4004020993118e-11	simple_aae		affected		R78G	single base exchange	rs1859788		show file
PILRA	polymorphism_automatic	2.4004020993118e-11	simple_aae		affected		R78G	single base exchange	rs1859788		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975996 (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)

chr7:99971834A>GN/A show variant in all transcripts IGV

HGNC symbol

PILRA

Ensembl transcript ID

ENST00000453419

Genbank transcript ID

N/A

UniProt peptide

Q9UKJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.232A>G
cDNA.431A>G
g.6682A>G

AA changes

R78G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs1859788

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1188	923	2111
ExAC	27836	-22905	4931

regulatory features

CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
NFKB, Transcription Factor, NFKB Transcription Factor Binding
Pax5, Transcription Factor, Pax5 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Rad21, Transcription Factor, Rad21 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.83	0.118
	0.956	0.114
(flanking)	0.903	0.09

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	6681	wt: 0.27 / mu: 0.97	wt: TTCCACAGGCAGTCC mu: TTCCACGGGCAGTCC	CCAC\|aggc

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019485

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000066684

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
20	197	TOPO_DOM	Extracellular (Potential).	lost
32	150	DOMAIN	Ig-like V-type.	lost
92	92	CONFLICT	D -> E (in Ref. 2; CAC01615).	might get lost (downstream of altered splice site)
100	100	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
219	303	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
267	272	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
269	269	MUTAGEN	Y->F: Greatly diminishes interaction with PTPN6.	might get lost (downstream of altered splice site)
281	281	CONFLICT	R -> K (in Ref. 1; AAD52964).	might get lost (downstream of altered splice site)
296	301	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

681 / 681

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

227 / 227

position of stopcodon in wt / mu cDNA

880 / 880

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

200 / 200

chromosome

strand

last intron/exon boundary

770

theoretical NMD boundary in CDS

520

length of CDS

681

coding sequence (CDS) position

232

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

431

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

6682

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

99971834

original gDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered gDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

original cDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered cDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

wildtype AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHRQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QGQQRTKATT PAREPFQNTE EPYENIRNEG
QNTDPKLNPK LHLTQSTSQP PSPQEPPERD PVLCLKGLTN GQPSQD*

mutated AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHGQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QGQQRTKATT PAREPFQNTE EPYENIRNEG
QNTDPKLNPK LHLTQSTSQP PSPQEPPERD PVLCLKGLTN GQPSQD*

speed

1.03 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: 0.999999999975996 (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)

chr7:99971834A>GN/A show variant in all transcripts IGV

HGNC symbol

PILRA

Ensembl transcript ID

ENST00000198536

Genbank transcript ID

NM_013439

UniProt peptide

Q9UKJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.232A>G
cDNA.444A>G
g.6682A>G

AA changes

R78G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs1859788

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1188	923	2111
ExAC	27836	-22905	4931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.83	0.118
	0.956	0.114
(flanking)	0.903	0.09

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	6681	wt: 0.27 / mu: 0.97	wt: TTCCACAGGCAGTCC mu: TTCCACGGGCAGTCC	CCAC\|aggc

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019485

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000066684

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
20	197	TOPO_DOM	Extracellular (Potential).	lost
32	150	DOMAIN	Ig-like V-type.	lost
92	92	CONFLICT	D -> E (in Ref. 2; CAC01615).	might get lost (downstream of altered splice site)
100	100	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
219	303	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
267	272	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
269	269	MUTAGEN	Y->F: Greatly diminishes interaction with PTPN6.	might get lost (downstream of altered splice site)
281	281	CONFLICT	R -> K (in Ref. 1; AAD52964).	might get lost (downstream of altered splice site)
296	301	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

912 / 912

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

304 / 304

position of stopcodon in wt / mu cDNA

1124 / 1124

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

213 / 213

chromosome

strand

last intron/exon boundary

1002

theoretical NMD boundary in CDS

739

length of CDS

912

coding sequence (CDS) position

232

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

444

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

6682

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

99971834

original gDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered gDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

original cDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered cDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

wildtype AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHRQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QAVTTTTQRP SSMTTTWRLS STTTTTGLRV
TQGKRRSDSW HISLETAVGV AVAVTVLGIM ILGLICLLRW RRRKGQQRTK ATTPAREPFQ
NTEEPYENIR NEGQNTDPKL NPKDDGIVYA SLALSSSTSP RAPPSHRPLK SPQNETLYSV
LKA*

mutated AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHGQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QAVTTTTQRP SSMTTTWRLS STTTTTGLRV
TQGKRRSDSW HISLETAVGV AVAVTVLGIM ILGLICLLRW RRRKGQQRTK ATTPAREPFQ
NTEEPYENIR NEGQNTDPKL NPKDDGIVYA SLALSSSTSP RAPPSHRPLK SPQNETLYSV
LKA*

speed

0.94 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975996 (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)

chr7:99971834A>GN/A show variant in all transcripts IGV

HGNC symbol

PILRA

Ensembl transcript ID

ENST00000394000

Genbank transcript ID

NM_178273

UniProt peptide

Q9UKJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.232A>G
cDNA.361A>G
g.6682A>G

AA changes

R78G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs1859788

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1188	923	2111
ExAC	27836	-22905	4931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.83	0.118
	0.956	0.114
(flanking)	0.903	0.09

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	6681	wt: 0.27 / mu: 0.97	wt: TTCCACAGGCAGTCC mu: TTCCACGGGCAGTCC	CCAC\|aggc

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019485

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000066684

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
20	197	TOPO_DOM	Extracellular (Potential).	lost
32	150	DOMAIN	Ig-like V-type.	lost
92	92	CONFLICT	D -> E (in Ref. 2; CAC01615).	might get lost (downstream of altered splice site)
100	100	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
219	303	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
267	272	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
269	269	MUTAGEN	Y->F: Greatly diminishes interaction with PTPN6.	might get lost (downstream of altered splice site)
281	281	CONFLICT	R -> K (in Ref. 1; AAD52964).	might get lost (downstream of altered splice site)
296	301	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

528 / 528

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

176 / 176

position of stopcodon in wt / mu cDNA

657 / 657

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

130 / 130

chromosome

strand

last intron/exon boundary

666

theoretical NMD boundary in CDS

486

length of CDS

528

coding sequence (CDS) position

232

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

361

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

6682

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

99971834

original gDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered gDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

original cDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered cDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

wildtype AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHRQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QGNPSKTQRS HMRISGMKDK IQIPS*

mutated AA sequence

MGRPLLLPLL PLLLPPAFLQ PSGSTGSGPS YLYGVTQPKH LSASMGGSVE IPFSFYYPWE
LATAPDVRIS WRRGHFHGQS FYSTRPPSIH KDYVNRLFLN WTEGQKSGFL RISNLQKQDQ
SVYFCRVELD TRSSGRQQWQ SIEGTKLSIT QGNPSKTQRS HMRISGMKDK IQIPS*

speed

1.18 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999975996 (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)

chr7:99971834A>GN/A show variant in all transcripts IGV

HGNC symbol

PILRA

Ensembl transcript ID

ENST00000350573

Genbank transcript ID

NM_178272

UniProt peptide

Q9UKJ1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.232A>G
cDNA.361A>G
g.6682A>G

AA changes

R78G Score: 125 explain score(s)

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

frameshift

known variant

Reference ID: rs1859788

database	homozygous (G/G)	heterozygous	allele carriers
1000G	1188	923	2111
ExAC	27836	-22905	4931

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.83	0.118
	0.956	0.114
(flanking)	0.903	0.09

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	6681	wt: 0.27 / mu: 0.97	wt: TTCCACAGGCAGTCC mu: TTCCACGGGCAGTCC	CCAC\|aggc

distance from splice site

168

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

not conserved

ENSPTRG00000019485

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000066684

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
20	197	TOPO_DOM	Extracellular (Potential).	lost
32	150	DOMAIN	Ig-like V-type.	lost
92	92	CONFLICT	D -> E (in Ref. 2; CAC01615).	might get lost (downstream of altered splice site)
100	100	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
198	218	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
219	303	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
267	272	MOTIF	ITIM motif 1.	might get lost (downstream of altered splice site)
269	269	MUTAGEN	Y->F: Greatly diminishes interaction with PTPN6.	might get lost (downstream of altered splice site)
281	281	CONFLICT	R -> K (in Ref. 1; AAD52964).	might get lost (downstream of altered splice site)
296	301	MOTIF	ITIM motif 2.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

693 / 693

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

231 / 231

position of stopcodon in wt / mu cDNA

822 / 822

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

130 / 130

chromosome

strand

last intron/exon boundary

700

theoretical NMD boundary in CDS

520

length of CDS

693

coding sequence (CDS) position

232

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

361

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

6682

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

99971834

original gDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered gDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

original cDNA sequence snippet

GGAGACGGGGCCACTTCCACAGGCAGTCCTTCTACAGCACA

altered cDNA sequence snippet

GGAGACGGGGCCACTTCCACGGGCAGTCCTTCTACAGCACA

wildtype AA sequence

mutated AA sequence

speed

1.17 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems