MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000368887
Querying Taster for transcript #2: ENST00000405485
MT speed 0 s - this script 3.766051 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PSTK	polymorphism_automatic	0.51387762020992	simple_aae		affected		G206R	single base exchange	rs3736582		show file
PSTK	polymorphism_automatic	0.51387762020992	simple_aae		affected		G206R	single base exchange	rs3736582		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.48612237979008 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:124742895G>CN/A show variant in all transcripts IGV

HGNC symbol

PSTK

Ensembl transcript ID

ENST00000368887

Genbank transcript ID

NM_153336

UniProt peptide

Q8IV42

alteration type

single base exchange

alteration region

CDS

DNA changes

c.616G>C
cDNA.1056G>C
g.28999G>C

AA changes

G206R Score: 125 explain score(s)

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

206

frameshift

known variant

Reference ID: rs3736582

database	homozygous (C/C)	heterozygous	allele carriers
1000G	882	1149	2031
ExAC	24917	-17067	7850

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.63	1
	0.939	0.713
(flanking)	-1.778	0

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 marginally increased	28999	wt: 0.8029 / mu: 0.8353 (marginal change - not scored)	wt: CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC mu: CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC	atgg\|GAAG
Donor marginally increased	28997	wt: 0.9969 / mu: 0.9975 (marginal change - not scored)	wt: CCTGATGGGAAGAAA mu: CCTGATGCGAAGAAA	TGAT\|ggga
Donor increased	29001	wt: 0.86 / mu: 0.98	wt: ATGGGAAGAAAGCTA mu: ATGCGAAGAAAGCTA	GGGA\|agaa
Donor marginally increased	28992	wt: 0.5994 / mu: 0.6460 (marginal change - not scored)	wt: ATCCACCTGATGGGA mu: ATCCACCTGATGCGA	CCAC\|ctga
Donor marginally increased	29002	wt: 0.7562 / mu: 0.8233 (marginal change - not scored)	wt: TGGGAAGAAAGCTAG mu: TGCGAAGAAAGCTAG	GGAA\|gaaa
Donor gained	28994	0.49	mu: CCACCTGATGCGAAG	ACCT\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

206

mutated

not conserved

206

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017858

206

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000063179

207

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0031041

157

ATR

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009556

191

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1047 / 1047

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

349 / 349

position of stopcodon in wt / mu cDNA

1487 / 1487

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

441 / 441

chromosome

strand

last intron/exon boundary

1489

theoretical NMD boundary in CDS

998

length of CDS

1047

coding sequence (CDS) position

616

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

1056

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

28999

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

124742895

original gDNA sequence snippet

CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC

altered gDNA sequence snippet

CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC

original cDNA sequence snippet

CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC

altered cDNA sequence snippet

CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC

wildtype AA sequence

MKTAENIRGT GSDGPRKRGL CVLCGLPAAG KSTFARALAH RLQQEQGWAI GVVAYDDVMP
DAFLAGARAR PAPSQWKLLR QELLKYLEYF LMAVINGCQM SVPPNRTEAM WEDFITCLKD
QDLIFSAAFE AQSCYLLTKT AVSRPLFLVL DDNFYYQSMR YEVYQLARKY SLGFCQLFLD
CPLETCLQRN GQRPQALPPE TIHLMGRKLE KPNPEKNAWE HNSLTIPSPA CASEASLEVT
DLLLTALENP VKYAEDNMEQ KDTDRIICST NILHKTDQTL RRIVSQTMKE AKGNQEAFSE
MTFKQRWVRA NHAAIWRIIL GNEHIKCRSA KVGWLQCCRI EKRPLSTG*

mutated AA sequence

MKTAENIRGT GSDGPRKRGL CVLCGLPAAG KSTFARALAH RLQQEQGWAI GVVAYDDVMP
DAFLAGARAR PAPSQWKLLR QELLKYLEYF LMAVINGCQM SVPPNRTEAM WEDFITCLKD
QDLIFSAAFE AQSCYLLTKT AVSRPLFLVL DDNFYYQSMR YEVYQLARKY SLGFCQLFLD
CPLETCLQRN GQRPQALPPE TIHLMRRKLE KPNPEKNAWE HNSLTIPSPA CASEASLEVT
DLLLTALENP VKYAEDNMEQ KDTDRIICST NILHKTDQTL RRIVSQTMKE AKGNQEAFSE
MTFKQRWVRA NHAAIWRIIL GNEHIKCRSA KVGWLQCCRI EKRPLSTG*

speed

0.80 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: 0.48612237979008 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:124742895G>CN/A show variant in all transcripts IGV

HGNC symbol

PSTK

Ensembl transcript ID

ENST00000405485

Genbank transcript ID

N/A

UniProt peptide

Q8IV42

alteration type

single base exchange

alteration region

CDS

DNA changes

c.616G>C
cDNA.682G>C
g.28999G>C

AA changes

G206R Score: 125 explain score(s)

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

206

frameshift

known variant

Reference ID: rs3736582

database	homozygous (C/C)	heterozygous	allele carriers
1000G	882	1149	2031
ExAC	24917	-17067	7850

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.63	1
	0.939	0.713
(flanking)	-1.778	0

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 marginally increased	28999	wt: 0.8029 / mu: 0.8353 (marginal change - not scored)	wt: CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC mu: CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC	atgg\|GAAG
Donor marginally increased	28997	wt: 0.9969 / mu: 0.9975 (marginal change - not scored)	wt: CCTGATGGGAAGAAA mu: CCTGATGCGAAGAAA	TGAT\|ggga
Donor increased	29001	wt: 0.86 / mu: 0.98	wt: ATGGGAAGAAAGCTA mu: ATGCGAAGAAAGCTA	GGGA\|agaa
Donor marginally increased	28992	wt: 0.5994 / mu: 0.6460 (marginal change - not scored)	wt: ATCCACCTGATGGGA mu: ATCCACCTGATGCGA	CCAC\|ctga
Donor marginally increased	29002	wt: 0.7562 / mu: 0.8233 (marginal change - not scored)	wt: TGGGAAGAAAGCTAG mu: TGCGAAGAAAGCTAG	GGAA\|gaaa
Donor gained	28994	0.49	mu: CCACCTGATGCGAAG	ACCT\|gatg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

206

mutated

not conserved

206

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017858

206

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000063179

207

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

not conserved

FBgn0031041

157

ATR

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000009556

191

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

870 / 870

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

290 / 290

position of stopcodon in wt / mu cDNA

936 / 936

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

67 / 67

chromosome

strand

last intron/exon boundary

1979

theoretical NMD boundary in CDS

1862

length of CDS

870

coding sequence (CDS) position

616

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

682

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

28999

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

124742895

original gDNA sequence snippet

CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC

altered gDNA sequence snippet

CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC

original cDNA sequence snippet

CTGAGACCATCCACCTGATGGGAAGAAAGCTAGAAAAGCCC

altered cDNA sequence snippet

CTGAGACCATCCACCTGATGCGAAGAAAGCTAGAAAAGCCC

wildtype AA sequence

mutated AA sequence

MKTAENIRGT GSDGPRKRGL CVLCGLPAAG KSTFARALAH RLQQEQGWAI GVVAYDDVMP
DAFLAGARAR PAPSQWKLLR QELLKYLEYF LMAVINGCQM SVPPNRTEAM WEDFITCLKD
QDLIFSAAFE AQSCYLLTKT AVSRPLFLVL DDNFYYQSMR YEVYQLARKY SLGFCQLFLD
CPLETCLQRN GQRPQALPPE TIHLMRRKLE KPNPEKNAWE HNSLTIPSPA CASEASLEVT
DLLLTALENP VKYAEDNMEQ KVNFQCKFNV NEKEQLFVGR SFEPNIKCE*

speed

0.77 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems