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: ENST00000304672
Querying Taster for transcript #2: ENST00000441198
Querying Taster for transcript #3: ENST00000446507
MT speed 2.92 s - this script 3.946177 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PTCRA	polymorphism_automatic	0.318527587147004	simple_aae		affected		V106I	single base exchange	rs9471966		show file
PTCRA	polymorphism_automatic	0.318527587147004	simple_aae		affected		V81I	single base exchange	rs9471966		show file
PTCRA	polymorphism_automatic	0.999999999999999	without_aae		affected			single base exchange	rs9471966		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.681472412852996 (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)

chr6:42891022G>AN/A show variant in all transcripts IGV

HGNC symbol

PTCRA

Ensembl transcript ID

ENST00000304672

Genbank transcript ID

NM_138296

UniProt peptide

Q6ISU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.316G>A
cDNA.397G>A
g.7296G>A

AA changes

V106I Score: 29 explain score(s)

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

106

frameshift

known variant

Reference ID: rs9471966

database	homozygous (A/A)	heterozygous	allele carriers
1000G	196	812	1008
ExAC	3893	21130	25023

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.098	0.991
	1.931	0.998
(flanking)	2.784	0.997

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
Acc increased	7299	wt: 0.69 / mu: 0.86	wt: CATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGGGCT mu: CATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGGGCT	gtct\|GCCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

106

mutated

all conserved

106

Ptroglodytes

all identical

ENSPTRG00000018176

Mmulatta

all identical

ENSMMUG00000000460

106

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036858

106

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
24	146	TOPO_DOM	Extracellular (Potential).	lost
104	109	STRAND		lost
107	107	DISULFID		might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
147	167	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
168	281	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
256	256	CONFLICT	A -> R (in Ref. 1; AAB06194, 2; AAC83346, 3; AAF89556 and 6; AAB18373).	might get lost (downstream of altered splice site)
269	269	CONFLICT	A -> R (in Ref. 1; AAB06194).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

846 / 846

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

282 / 282

position of stopcodon in wt / mu cDNA

927 / 927

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

82 / 82

chromosome

strand

last intron/exon boundary

506

theoretical NMD boundary in CDS

374

length of CDS

846

coding sequence (CDS) position

316

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

397

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

7296

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

42891022

original gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGG

altered gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGG

original cDNA sequence snippet

TGGCATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGG

altered cDNA sequence snippet

TGGCATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGG

wildtype AA sequence

MAGTWLLLLL ALGCPALPTG VGGTPFPSLA PPIMLLVDGK QQMVVVCLVL DVAPPGLDSP
IWFSAGNGSA LDAFTYGPSP ATDGTWTNLA HLSLPSEELA SWEPLVCHTG PGAEGHSRST
QPMHLSGEAS TARTCPQEPL RGTPGGALWL GVLRLLLFKL LLFDLLLTCS CLCDPAGPLP
SPATTTRLRA LGSHRLHPAT ETGGREATSS PRPQPRDRRW GDTPPGRKPG SPVWGEGSYL
SSYPTCPAQA WCSRSALRAP SSSLGAFFAG DLPPPLQAGA A*

mutated AA sequence

MAGTWLLLLL ALGCPALPTG VGGTPFPSLA PPIMLLVDGK QQMVVVCLVL DVAPPGLDSP
IWFSAGNGSA LDAFTYGPSP ATDGTWTNLA HLSLPSEELA SWEPLICHTG PGAEGHSRST
QPMHLSGEAS TARTCPQEPL RGTPGGALWL GVLRLLLFKL LLFDLLLTCS CLCDPAGPLP
SPATTTRLRA LGSHRLHPAT ETGGREATSS PRPQPRDRRW GDTPPGRKPG SPVWGEGSYL
SSYPTCPAQA WCSRSALRAP SSSLGAFFAG DLPPPLQAGA A*

speed

1.04 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: 0.681472412852996 (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)

chr6:42891022G>AN/A show variant in all transcripts IGV

HGNC symbol

PTCRA

Ensembl transcript ID

ENST00000441198

Genbank transcript ID

NM_001243169

UniProt peptide

Q6ISU1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.241G>A
cDNA.322G>A
g.7296G>A

AA changes

V81I Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs9471966

database	homozygous (A/A)	heterozygous	allele carriers
1000G	196	812	1008
ExAC	3893	21130	25023

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.098	0.991
	1.931	0.998
(flanking)	2.784	0.997

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
Acc increased	7299	wt: 0.69 / mu: 0.86	wt: CATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGGGCT mu: CATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGGGCT	gtct\|GCCA

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 identical

ENSPTRG00000018176

Mmulatta

all identical

ENSMMUG00000000460

106

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000036858

106

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
24	146	TOPO_DOM	Extracellular (Potential).	lost
79	81	STRAND		lost
82	84	TURN		might get lost (downstream of altered splice site)
85	95	STRAND		might get lost (downstream of altered splice site)
96	100	HELIX		might get lost (downstream of altered splice site)
104	109	STRAND		might get lost (downstream of altered splice site)
107	107	DISULFID		might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
147	167	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
168	281	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
256	256	CONFLICT	A -> R (in Ref. 1; AAB06194, 2; AAC83346, 3; AAF89556 and 6; AAB18373).	might get lost (downstream of altered splice site)
269	269	CONFLICT	A -> R (in Ref. 1; AAB06194).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

771 / 771

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

257 / 257

position of stopcodon in wt / mu cDNA

852 / 852

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

82 / 82

chromosome

strand

last intron/exon boundary

431

theoretical NMD boundary in CDS

299

length of CDS

771

coding sequence (CDS) position

241

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

322

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

7296

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

42891022

original gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGG

altered gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGG

original cDNA sequence snippet

TGGCATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGG

altered cDNA sequence snippet

TGGCATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGG

wildtype AA sequence

MAGTWLLLLL ALGCPALPTG PVSFPSSPEA ATTGPIWFSA GNGSALDAFT YGPSPATDGT
WTNLAHLSLP SEELASWEPL VCHTGPGAEG HSRSTQPMHL SGEASTARTC PQEPLRGTPG
GALWLGVLRL LLFKLLLFDL LLTCSCLCDP AGPLPSPATT TRLRALGSHR LHPATETGGR
EATSSPRPQP RDRRWGDTPP GRKPGSPVWG EGSYLSSYPT CPAQAWCSRS ALRAPSSSLG
AFFAGDLPPP LQAGAA*

mutated AA sequence

MAGTWLLLLL ALGCPALPTG PVSFPSSPEA ATTGPIWFSA GNGSALDAFT YGPSPATDGT
WTNLAHLSLP SEELASWEPL ICHTGPGAEG HSRSTQPMHL SGEASTARTC PQEPLRGTPG
GALWLGVLRL LLFKLLLFDL LLTCSCLCDP AGPLPSPATT TRLRALGSHR LHPATETGGR
EATSSPRPQP RDRRWGDTPP GRKPGSPVWG EGSYLSSYPT CPAQAWCSRS ALRAPSSSLG
AFFAGDLPPP LQAGAA*

speed

1.10 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 1.4384912185419e-15 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

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)

chr6:42891022G>AN/A show variant in all transcripts IGV

HGNC symbol

PTCRA

Ensembl transcript ID

ENST00000446507

Genbank transcript ID

NM_001243170

UniProt peptide

Q6ISU1

alteration type

single base exchange

alteration region

intron

DNA changes

g.7296G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs9471966

database	homozygous (A/A)	heterozygous	allele carriers
1000G	196	812	1008
ExAC	3893	21130	25023

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.098	0.991
	1.931	0.998
(flanking)	2.784	0.997

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
Acc increased	7299	wt: 0.69 / mu: 0.86	wt: CATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGGGCT mu: CATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGGGCT	gtct\|GCCA

distance from splice site

945

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	23	SIGNAL	Potential.	might get lost (downstream of altered splice site)
24	146	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
33	52	STRAND		might get lost (downstream of altered splice site)
47	47	DISULFID		might get lost (downstream of altered splice site)
62	64	STRAND		might get lost (downstream of altered splice site)
66	68	STRAND		might get lost (downstream of altered splice site)
67	67	CARBOHYD	N-linked (GlcNAc...).	might get lost (downstream of altered splice site)
79	81	STRAND		might get lost (downstream of altered splice site)
82	84	TURN		might get lost (downstream of altered splice site)
85	95	STRAND		might get lost (downstream of altered splice site)
96	100	HELIX		might get lost (downstream of altered splice site)
104	109	STRAND		might get lost (downstream of altered splice site)
107	107	DISULFID		might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
135	135	DISULFID	Interchain (with TCRB) (Probable).	might get lost (downstream of altered splice site)
147	167	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
168	281	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
256	256	CONFLICT	A -> R (in Ref. 1; AAB06194, 2; AAC83346, 3; AAF89556 and 6; AAB18373).	might get lost (downstream of altered splice site)
269	269	CONFLICT	A -> R (in Ref. 1; AAB06194).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

82 / 82

chromosome

strand

last intron/exon boundary

185

theoretical NMD boundary in CDS

length of CDS

525

coding sequence (CDS) position

N/A

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

N/A

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

7296

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

42891022

original gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGGTCTGCCACACTGGGCCTGGG

altered gDNA sequence snippet

TGGCATCCTGGGAGCCTTTGATCTGCCACACTGGGCCTGGG

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MAGTWLLLLL ALGCPALPTG EASTARTCPQ EPLRGTPGGA LWLGVLRLLL FKLLLFDLLL
TCSCLCDPAG PLPSPATTTR LRALGSHRLH PATETGGREA TSSPRPQPRD RRWGDTPPGR
KPGSPVWGEG SYLSSYPTCP AQAWCSRSAL RAPSSSLGAF FAGDLPPPLQ AGAA*

mutated AA sequence

N/A

speed

0.78 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