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: ENST00000448504
Querying Taster for transcript #2: ENST00000452479
MT speed 0 s - this script 4.642835 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ARSG	polymorphism_automatic	1.00493946497693e-10	simple_aae				W274R	single base exchange	rs1558878		show file
ARSG	polymorphism_automatic	1.00493946497693e-10	simple_aae				W110R	single base exchange	rs1558878		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999899506 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:66364804T>CN/A show variant in all transcripts IGV

HGNC symbol

ARSG

Ensembl transcript ID

ENST00000448504

Genbank transcript ID

NM_001267727

UniProt peptide

Q96EG1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.820T>C
cDNA.1616T>C
g.109482T>C

AA changes

W274R Score: 101 explain score(s)

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

274

frameshift

known variant

Reference ID: rs1558878

database	homozygous (C/C)	heterozygous	allele carriers
1000G	348	1104	1452
ExAC	12437	7893	20330

regulatory features

Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.13	0.309
	0.567	0.301
(flanking)	-0.057	0.294

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 marginally increased	109484	wt: 0.9818 / mu: 0.9915 (marginal change - not scored)	wt: CTCTGGGAGATGGAC mu: CTCCGGGAGATGGAC	CTGG\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

274

mutated

not conserved

274

Ptroglodytes

not conserved

ENSPTRG00000009577

274

Mmulatta

not conserved

ENSMMUG00000007306

274

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000020604

274

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016680

284

Drerio

not conserved

ENSDARG00000052534

278

Dmelanogaster

no homologue

Celegans

not conserved

D1014.1

266

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1578 / 1578

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

526 / 526

position of stopcodon in wt / mu cDNA

2374 / 2374

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

797 / 797

chromosome

strand

last intron/exon boundary

2100

theoretical NMD boundary in CDS

1253

length of CDS

1578

coding sequence (CDS) position

820

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

1616

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

109482

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

66364804

original gDNA sequence snippet

GCCTGTATGGTGCAGGGCTCTGGGAGATGGACAGTCTGGTG

altered gDNA sequence snippet

GCCTGTATGGTGCAGGGCTCCGGGAGATGGACAGTCTGGTG

original cDNA sequence snippet

GCCTGTATGGTGCAGGGCTCTGGGAGATGGACAGTCTGGTG

altered cDNA sequence snippet

GCCTGTATGGTGCAGGGCTCCGGGAGATGGACAGTCTGGTG

wildtype AA sequence

MGWLFLKVLL AGVSFSGFLY PLVDFCISGK TRGQKPNFVI ILADDMGWGD LGANWAETKD
TANLDKMASE GMRFVDFHAA ASTCSPSRAS LLTGRLGLRN GVTRNFAVTS VGGLPLNETT
LAEVLQQAGY VTGIIGKWHL GHHGSYHPNF RGFDYYFGIP YSHDMGCTDT PGYNHPPCPA
CPQGDGPSRN LQRDCYTDVA LPLYENLNIV EQPVNLSSLA QKYAEKATQF IQRASTSGRP
FLLYVALAHM HVPLPVTQLP AAPRGRSLYG AGLWEMDSLV GQIKDKVDHT VKENTFLWFT
GDNGPWAQKC ELAGSVGPFT GFWQTRQGGS PAKQTTWEGG HRVPALAYWP GRVPVNVTST
ALLSVLDIFP TVVALAQASL PQGRRFDGVD VSEVLFGRSQ PGHRVLFHPN SGAAGEFGAL
QTVRLERYKA FYITGGARAC DGSTGPELQH KFPLIFNLED DTAEAVPLER GGAEYQAVLP
EVRKVLADVL QDIANDNISS ADYTQDPSVT PCCNPYQIAC RCQAA*

mutated AA sequence

MGWLFLKVLL AGVSFSGFLY PLVDFCISGK TRGQKPNFVI ILADDMGWGD LGANWAETKD
TANLDKMASE GMRFVDFHAA ASTCSPSRAS LLTGRLGLRN GVTRNFAVTS VGGLPLNETT
LAEVLQQAGY VTGIIGKWHL GHHGSYHPNF RGFDYYFGIP YSHDMGCTDT PGYNHPPCPA
CPQGDGPSRN LQRDCYTDVA LPLYENLNIV EQPVNLSSLA QKYAEKATQF IQRASTSGRP
FLLYVALAHM HVPLPVTQLP AAPRGRSLYG AGLREMDSLV GQIKDKVDHT VKENTFLWFT
GDNGPWAQKC ELAGSVGPFT GFWQTRQGGS PAKQTTWEGG HRVPALAYWP GRVPVNVTST
ALLSVLDIFP TVVALAQASL PQGRRFDGVD VSEVLFGRSQ PGHRVLFHPN SGAAGEFGAL
QTVRLERYKA FYITGGARAC DGSTGPELQH KFPLIFNLED DTAEAVPLER GGAEYQAVLP
EVRKVLADVL QDIANDNISS ADYTQDPSVT PCCNPYQIAC RCQAA*

speed

1.35 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: 0.999999999899506 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:66364804T>CN/A show variant in all transcripts IGV

HGNC symbol

ARSG

Ensembl transcript ID

ENST00000452479

Genbank transcript ID

N/A

UniProt peptide

Q96EG1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.328T>C
cDNA.653T>C
g.109482T>C

AA changes

W110R Score: 101 explain score(s)

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

110

frameshift

known variant

Reference ID: rs1558878

database	homozygous (C/C)	heterozygous	allele carriers
1000G	348	1104	1452
ExAC	12437	7893	20330

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.13	0.309
	0.567	0.301
(flanking)	-0.057	0.294

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 marginally increased	109484	wt: 0.9818 / mu: 0.9915 (marginal change - not scored)	wt: CTCTGGGAGATGGAC mu: CTCCGGGAGATGGAC	CTGG\|gaga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

110

mutated

not conserved

110

Ptroglodytes

not conserved

ENSPTRG00000009577

274

Mmulatta

not conserved

ENSMMUG00000007306

274

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000020604

274

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016680

284

Drerio

not conserved

ENSDARG00000052534

274

Dmelanogaster

no homologue

Celegans

not conserved

D1014.1

266

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1086 / 1086

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

362 / 362

position of stopcodon in wt / mu cDNA

1411 / 1411

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

326 / 326

chromosome

strand

last intron/exon boundary

1137

theoretical NMD boundary in CDS

761

length of CDS

1086

coding sequence (CDS) position

328

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

653

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

109482

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

66364804

original gDNA sequence snippet

GCCTGTATGGTGCAGGGCTCTGGGAGATGGACAGTCTGGTG

altered gDNA sequence snippet

GCCTGTATGGTGCAGGGCTCCGGGAGATGGACAGTCTGGTG

original cDNA sequence snippet

GCCTGTATGGTGCAGGGCTCTGGGAGATGGACAGTCTGGTG

altered cDNA sequence snippet

GCCTGTATGGTGCAGGGCTCCGGGAGATGGACAGTCTGGTG

wildtype AA sequence

MGCTDTPGYN HPPCPACPQG DGPSRNLQRD CYTDVALPLY ENLNIVEQPV NLSSLAQKYA
EKATQFIQRA STSGRPFLLY VALAHMHVPL PVTQLPAAPR GRSLYGAGLW EMDSLVGQIK
DKVDHTVKEN TFLWFTGDNG PWAQKCELAG SVGPFTGFWQ TRQGGSPAKQ TTWEGGHRVP
ALAYWPGRVP VNVTSTALLS VLDIFPTVVA LAQASLPQGR RFDGVDVSEV LFGRSQPGHR
VLFHPNSGAA GEFGALQTVR LERYKAFYIT GGARACDGST GPELQHKFPL IFNLEDDTAE
AVPLERGGAE YQAVLPEVRK VLADVLQDIA NDNISSADYT QDPSVTPCCN PYQIACRCQA
A*

mutated AA sequence

MGCTDTPGYN HPPCPACPQG DGPSRNLQRD CYTDVALPLY ENLNIVEQPV NLSSLAQKYA
EKATQFIQRA STSGRPFLLY VALAHMHVPL PVTQLPAAPR GRSLYGAGLR EMDSLVGQIK
DKVDHTVKEN TFLWFTGDNG PWAQKCELAG SVGPFTGFWQ TRQGGSPAKQ TTWEGGHRVP
ALAYWPGRVP VNVTSTALLS VLDIFPTVVA LAQASLPQGR RFDGVDVSEV LFGRSQPGHR
VLFHPNSGAA GEFGALQTVR LERYKAFYIT GGARACDGST GPELQHKFPL IFNLEDDTAE
AVPLERGGAE YQAVLPEVRK VLADVLQDIA NDNISSADYT QDPSVTPCCN PYQIACRCQA
A*

speed

1.34 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems