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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000284881
Querying Taster for transcript #2: ENST00000400559
MT speed 0 s - this script 3.437 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
C21orf91	polymorphism_automatic	0.990384043499333	simple_aae		affected		D136E	single base exchange	rs1047978		show file
C21orf91	polymorphism_automatic	0.990384043499333	simple_aae		affected		D136E	single base exchange	rs1047978		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.00961595650066682 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM119356)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr21:19169155G>CN/A show variant in all transcripts IGV

HGNC symbol

C21orf91

Ensembl transcript ID

ENST00000284881

Genbank transcript ID

NM_001100420

UniProt peptide

Q9NYK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.408C>G
cDNA.499C>G
g.22549C>G

AA changes

D136E Score: 45 explain score(s)

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

136

frameshift

known variant

Reference ID: rs1047978

database	homozygous (C/C)	heterozygous	allele carriers
1000G	213	879	1092
ExAC	6589	19589	26178

known disease mutation at this position, please check HGMD for details (HGMD ID CM119356)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
FOXA2, Transcription Factor, FOXA2 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
HNF4A, Transcription Factor, HNF4A Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.979	1
	0.539	1
(flanking)	2.866	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 marginally increased	22550	wt: 0.9600 / mu: 0.9614 (marginal change - not scored)	wt: TTGACTCCCAAGTAC mu: TTGAGTCCCAAGTAC	GACT\|ccca
Acc gained	22548	0.75	mu: AAAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATT	ttga\|GTCC
Donor gained	22543	0.97	mu: CCACAGTTTGAGTCC	ACAG\|tttg

distance from splice site

257

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

136

mutated

all conserved

136

Ptroglodytes

all identical

ENSPTRG00000013798

136

Mmulatta

all identical

ENSMMUG00000019155

136

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022864

136

Ggallus

all identical

ENSGALG00000015716

135

Trubripes

no homologue

Drerio

all identical

ENSDARG00000030803

136

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002049

139

protein features

start (aa)	end (aa)	feature	details
214	214	CONFLICT	H -> Y (in Ref. 2; BAB14691).	might get lost (downstream of altered splice site)
249	249	CONFLICT	T -> P (in Ref. 2; BAB14691).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

894 / 894

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

298 / 298

position of stopcodon in wt / mu cDNA

985 / 985

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

92 / 92

chromosome

strand

-1

last intron/exon boundary

819

theoretical NMD boundary in CDS

677

length of CDS

894

coding sequence (CDS) position

408

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

499

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

22549

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

19169155

original gDNA sequence snippet

AAATTACTCCCACAGTTTGACTCCCAAGTACCAAAATATTC

altered gDNA sequence snippet

AAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATTC

original cDNA sequence snippet

AAATTACTCCCACAGTTTGACTCCCAAGTACCAAAATATTC

altered cDNA sequence snippet

AAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATTC

wildtype AA sequence

MNEEEQFVNI DLNDDNICSV CKLGTDKETL SFCHICFELN IEGVPKSDLL HTKSLRGHKD
CFEKYHLIAN QGCPRSKLSK STYEEVKTIL SKKINWIVQY AQNKDLDSDS ECSKNPQHHL
FNFRHKPEEK LLPQFDSQVP KYSAKWIDGS AGGISNCTQR ILEQRENTDF GLSMLQDSGA
TLCRNSVLWP HSHNQAQKKE ETISSPEANV QTQHPHYSRE ELNSMTLGEV EQLNAKLLQQ
IQEVFEELTH QVQEKDSLAS QLHVRHVAIE QLLKNCSKLP CLQVGRTGMK SHLPINN*

mutated AA sequence

MNEEEQFVNI DLNDDNICSV CKLGTDKETL SFCHICFELN IEGVPKSDLL HTKSLRGHKD
CFEKYHLIAN QGCPRSKLSK STYEEVKTIL SKKINWIVQY AQNKDLDSDS ECSKNPQHHL
FNFRHKPEEK LLPQFESQVP KYSAKWIDGS AGGISNCTQR ILEQRENTDF GLSMLQDSGA
TLCRNSVLWP HSHNQAQKKE ETISSPEANV QTQHPHYSRE ELNSMTLGEV EQLNAKLLQQ
IQEVFEELTH QVQEKDSLAS QLHVRHVAIE QLLKNCSKLP CLQVGRTGMK SHLPINN*

speed

0.09 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: 0.00961595650066682 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM119356)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr21:19169155G>CN/A show variant in all transcripts IGV

HGNC symbol

C21orf91

Ensembl transcript ID

ENST00000400559

Genbank transcript ID

NM_017447

UniProt peptide

Q9NYK6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.408C>G
cDNA.499C>G
g.22549C>G

AA changes

D136E Score: 45 explain score(s)

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

136

frameshift

known variant

Reference ID: rs1047978

database	homozygous (C/C)	heterozygous	allele carriers
1000G	213	879	1092
ExAC	6589	19589	26178

known disease mutation at this position, please check HGMD for details (HGMD ID CM119356)

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.979	1
	0.539	1
(flanking)	2.866	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 marginally increased	22550	wt: 0.9600 / mu: 0.9614 (marginal change - not scored)	wt: TTGACTCCCAAGTAC mu: TTGAGTCCCAAGTAC	GACT\|ccca
Acc gained	22548	0.75	mu: AAAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATT	ttga\|GTCC
Donor gained	22543	0.97	mu: CCACAGTTTGAGTCC	ACAG\|tttg

distance from splice site

257

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

136

mutated

all conserved

136

Ptroglodytes

all identical

ENSPTRG00000013798

136

Mmulatta

all identical

ENSMMUG00000019155

136

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000022864

136

Ggallus

all identical

ENSGALG00000015716

135

Trubripes

no homologue

Drerio

all identical

ENSDARG00000030803

136

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000002049

139

protein features

start (aa)	end (aa)	feature	details
214	214	CONFLICT	H -> Y (in Ref. 2; BAB14691).	might get lost (downstream of altered splice site)
249	249	CONFLICT	T -> P (in Ref. 2; BAB14691).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

891 / 891

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

297 / 297

position of stopcodon in wt / mu cDNA

982 / 982

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

92 / 92

chromosome

strand

-1

last intron/exon boundary

819

theoretical NMD boundary in CDS

677

length of CDS

891

coding sequence (CDS) position

408

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

499

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

22549

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

19169155

original gDNA sequence snippet

AAATTACTCCCACAGTTTGACTCCCAAGTACCAAAATATTC

altered gDNA sequence snippet

AAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATTC

original cDNA sequence snippet

AAATTACTCCCACAGTTTGACTCCCAAGTACCAAAATATTC

altered cDNA sequence snippet

AAATTACTCCCACAGTTTGAGTCCCAAGTACCAAAATATTC

wildtype AA sequence

MNEEEQFVNI DLNDDNICSV CKLGTDKETL SFCHICFELN IEGVPKSDLL HTKSLRGHKD
CFEKYHLIAN QGCPRSKLSK STYEEVKTIL SKKINWIVQY AQNKDLDSDS ECSKNPQHHL
FNFRHKPEEK LLPQFDSQVP KYSAKWIDGS AGGISNCTQR ILEQRENTDF GLSMLQDSGA
TLCRNSVLWP HSHNQAQKKE ETISSPEANV QTQHPHYSRE ELNSMTLGEV EQLNAKLLQQ
IQVFEELTHQ VQEKDSLASQ LHVRHVAIEQ LLKNCSKLPC LQVGRTGMKS HLPINN*

mutated AA sequence

MNEEEQFVNI DLNDDNICSV CKLGTDKETL SFCHICFELN IEGVPKSDLL HTKSLRGHKD
CFEKYHLIAN QGCPRSKLSK STYEEVKTIL SKKINWIVQY AQNKDLDSDS ECSKNPQHHL
FNFRHKPEEK LLPQFESQVP KYSAKWIDGS AGGISNCTQR ILEQRENTDF GLSMLQDSGA
TLCRNSVLWP HSHNQAQKKE ETISSPEANV QTQHPHYSRE ELNSMTLGEV EQLNAKLLQQ
IQVFEELTHQ VQEKDSLASQ LHVRHVAIEQ LLKNCSKLPC LQVGRTGMKS HLPINN*

speed

1.32 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems