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: ENST00000311916
Querying Taster for transcript #2: ENST00000370228
MT speed 0 s - this script 3.506391 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
TWNK	disease_causing_automatic	0.999981258841193	simple_aae		affected	0	A318T	single base exchange	rs80356542		show file
TWNK	disease_causing_automatic	0.999981258841193	simple_aae		affected	0	A318T	single base exchange	rs80356542		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999981258841193 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM074977)
known disease mutation: rs4630 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:102748919G>AN/A show variant in all transcripts IGV

HGNC symbol

TWNK

Ensembl transcript ID

ENST00000311916

Genbank transcript ID

NM_001163813

UniProt peptide

Q96RR1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.952G>A
cDNA.1137G>A
g.1796G>A

AA changes

A318T Score: 58 explain score(s)

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

318

frameshift

known variant

Reference ID: rs80356542
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs4630 (pathogenic for Infantile onset spinocerebellar ataxia) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074977)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074977)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074977)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.227	0.965
	3.587	1
(flanking)	5.972	1

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	1792	wt: 0.28 / mu: 0.88	wt: TGGGAAGCCGCCAAG mu: TGGGAAGCCACCAAG	GGAA\|gccg

distance from splice site

292

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

318

mutated

not conserved

318

Ptroglodytes

no alignment

ENSPTRG00000029751

n/a

Mmulatta

all identical

ENSMMUG00000010677

318

Fcatus

all identical

ENSFCAG00000015694

318

Mmusculus

all identical

ENSMUSG00000025209

319

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0032154

284

Celegans

all identical

F46G11.1

232

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
351	351	CONFLICT	N -> D (in Ref. 3; CAE45905).	might get lost (downstream of altered splice site)
384	635	DOMAIN	SF4 helicase.	might get lost (downstream of altered splice site)
415	422	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2055 / 2055

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

685 / 685

position of stopcodon in wt / mu cDNA

2240 / 2240

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

186 / 186

chromosome

strand

last intron/exon boundary

1920

theoretical NMD boundary in CDS

1684

length of CDS

2055

coding sequence (CDS) position

952

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

1137

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

1796

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

102748919

original gDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCGCCAAGTTGTTTGCACGAAAA

altered gDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCACCAAGTTGTTTGCACGAAAA

original cDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCGCCAAGTTGTTTGCACGAAAA

altered cDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCACCAAGTTGTTTGCACGAAAA

wildtype AA sequence

MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEAAKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLTQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKAS QEADNVLILQ DRKLVTGPGK
RYLQVSKNRF DGDVGVFPLE FNKNSLTFSI PPKNKARLKK IKDDTGPVAK KPSSGKKGAT
TQNSEICSGQ APTPDQPDTS KRSK*

mutated AA sequence

MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEATKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLTQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKAS QEADNVLILQ DRKLVTGPGK
RYLQVSKNRF DGDVGVFPLE FNKNSLTFSI PPKNKARLKK IKDDTGPVAK KPSSGKKGAT
TQNSEICSGQ APTPDQPDTS KRSK*

speed

0.75 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

disease causing

Model: simple_aae, prob: 0.999981258841193 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM074977)
known disease mutation: rs4630 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:102748919G>AN/A show variant in all transcripts IGV

HGNC symbol

TWNK

Ensembl transcript ID

ENST00000370228

Genbank transcript ID

NM_001163812

UniProt peptide

Q96RR1

alteration type

single base exchange

alteration region

CDS

DNA changes

c.952G>A
cDNA.1137G>A
g.1796G>A

AA changes

A318T Score: 58 explain score(s)

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

318

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.227	0.965
	3.587	1
(flanking)	5.972	1

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	1792	wt: 0.28 / mu: 0.88	wt: TGGGAAGCCGCCAAG mu: TGGGAAGCCACCAAG	GGAA\|gccg

distance from splice site

292

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

318

mutated

not conserved

318

Ptroglodytes

no alignment

ENSPTRG00000029751

n/a

Mmulatta

all identical

ENSMMUG00000010677

318

Fcatus

all identical

ENSFCAG00000015694

318

Mmusculus

all identical

ENSMUSG00000025209

319

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

all identical

FBgn0032154

284

Celegans

all identical

F46G11.1

232

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
351	351	CONFLICT	N -> D (in Ref. 3; CAE45905).	might get lost (downstream of altered splice site)
384	635	DOMAIN	SF4 helicase.	might get lost (downstream of altered splice site)
415	422	NP_BIND	ATP (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1749 / 1749

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

583 / 583

position of stopcodon in wt / mu cDNA

1934 / 1934

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

186 / 186

chromosome

strand

last intron/exon boundary

1964

theoretical NMD boundary in CDS

1728

length of CDS

1749

coding sequence (CDS) position

952

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

1137

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

1796

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

102748919

original gDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCGCCAAGTTGTTTGCACGAAAA

altered gDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCACCAAGTTGTTTGCACGAAAA

original cDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCGCCAAGTTGTTTGCACGAAAA

altered cDNA sequence snippet

ACCTTCGGTCCTGGGAAGCCACCAAGTTGTTTGCACGAAAA

wildtype AA sequence

mutated AA sequence

MWVLLRSGYP LRILLPLRGE WMGRRGLPRN LAPGPPRRRY RKETLQALDM PVLPVTATEI
RQYLRGHGIP FQDGHSCLRA LSPFAESSQL KGQTGVTTSF SLFIDKTTGH FLCMTSLAEG
SWEDFQASVE GRGDGAREGF LLSKAPEFED SEEVRRIWNR AIPLWELPDQ EEVQLADTMF
GLTKVTDDTL KRFSVRYLRP ARSLVFPWFS PGGSGLRGLK LLEAKCQGDG VSYEETTIPR
PSAYHNLFGL PLISRRDAEV VLTSRELDSL ALNQSTGLPT LTLPRGTTCL PPALLPYLEQ
FRRIVFWLGD DLRSWEATKL FARKLNPKRC FLVRPGDQQP RPLEALNGGF NLSRILRTAL
PAWHKSIVSF RQLREEVLGE LSNVEQAAGL RWSRFPDLNR ILKGHRKGEL TVFTGPTGSG
KTTFISEYAL DLCSQGVNTL WGSFEISNVR LARVMLTQFA EGRLEDQLDK YDHWADRFED
LPLYFMTFHG QQSIRTVIDT MQHAVYVYDI CHVIIDNLQF MMGHEQLSTD RIAAQDYIIG
VFRKFATDNN CHVTLVIHPR KEDDDKELQT ASIFGSAKVS GL*

speed

0.76 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems