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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000256996
Querying Taster for transcript #2: ENST00000378603
Querying Taster for transcript #3: ENST00000378600
Querying Taster for transcript #4: ENST00000378601
MT speed 0 s - this script 5.494134 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
DDB2	disease_causing_automatic	0.999999896073419	simple_aae			0	R209H	single base exchange	rs121434640		show file
DDB2	disease_causing_automatic	0.999999974251918	simple_aae			0	R273H	single base exchange	rs121434640		show file
DDB2	disease_causing_automatic	1	without_aae			0		single base exchange	rs121434640		show file
DDB2	disease_causing_automatic	1	without_aae			0		single base exchange	rs121434640		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999896073419 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960485)
known disease mutation: rs8788 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256423G>AN/A show variant in all transcripts IGV

HGNC symbol

DDB2

Ensembl transcript ID

ENST00000378603

Genbank transcript ID

N/A

UniProt peptide

Q92466

alteration type

single base exchange

alteration region

CDS

DNA changes

c.626G>A
cDNA.821G>A
g.19931G>A

AA changes

R209H Score: 29 explain score(s)

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

209

frameshift

known variant

Reference ID: rs121434640

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

known disease mutation: rs8788 (pathogenic for Xeroderma pigmentosum, group E) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960485)

regulatory features

CBP, Transcription Factor, CBP Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.874	1
	4.531	1
(flanking)	1.33	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	19934	wt: 0.8419 / mu: 0.9148 (marginal change - not scored)	wt: GCGCCAGGTTAGAGG mu: GCACCAGGTTAGAGG	GCCA\|ggtt
Donor marginally increased	19936	wt: 0.4054 / mu: 0.4390 (marginal change - not scored)	wt: GCCAGGTTAGAGGGA mu: ACCAGGTTAGAGGGA	CAGG\|ttag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

209

mutated

not conserved

209

Ptroglodytes

all identical

ENSPTRG00000003558

273

Mmulatta

all identical

ENSMMUG00000022964

273

Fcatus

all identical

ENSFCAG00000002526

273

Mmusculus

all identical

ENSMUSG00000002109

273

Ggallus

all identical

ENSGALG00000008218

293

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041140

282

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003980

282

protein features

start (aa)	end (aa)	feature	details
207	210	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1092 / 1092

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

364 / 364

position of stopcodon in wt / mu cDNA

1287 / 1287

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

196 / 196

chromosome

strand

last intron/exon boundary

1238

theoretical NMD boundary in CDS

992

length of CDS

1092

coding sequence (CDS) position

626

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

821

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

19931

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

47256423

original gDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered gDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

original cDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered cDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

wildtype AA sequence

MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQIG AGGSITGLKF NPLNTNQFYA SSMEGTTRLQ
DFKGNILRVF ASSDTINIWF CSLDVSASSR MVVTGDNVGN VILLNMDGKE LWNLRMHKKK
VTHVALNPCC DWFLATASVD QTVKIWDLRQ VRGKASFLYS LPHRHPVNAA CFSPDGARLL
TTDQKSEIRV YSASQWDCPL GLIPHPHRHF QHLTPIKAAW HPRYNLIVVG RYPDPNFKSC
TPYELRTIDV FDGNSGKMMC QLYDPESSGI SSLNEFNPMG DTLASAMGYH ILIWSQEEAR
TRK*

mutated AA sequence

MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQIG AGGSITGLKF NPLNTNQFYA SSMEGTTRLQ
DFKGNILRVF ASSDTINIWF CSLDVSASSR MVVTGDNVGN VILLNMDGKE LWNLRMHKKK
VTHVALNPCC DWFLATASVD QTVKIWDLHQ VRGKASFLYS LPHRHPVNAA CFSPDGARLL
TTDQKSEIRV YSASQWDCPL GLIPHPHRHF QHLTPIKAAW HPRYNLIVVG RYPDPNFKSC
TPYELRTIDV FDGNSGKMMC QLYDPESSGI SSLNEFNPMG DTLASAMGYH ILIWSQEEAR
TRK*

speed

1.33 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: 0.999999974251918 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960485)
known disease mutation: rs8788 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256423G>AN/A show variant in all transcripts IGV

HGNC symbol

DDB2

Ensembl transcript ID

ENST00000256996

Genbank transcript ID

NM_000107

UniProt peptide

Q92466

alteration type

single base exchange

alteration region

CDS

DNA changes

c.818G>A
cDNA.1013G>A
g.19931G>A

AA changes

R273H Score: 29 explain score(s)

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

273

frameshift

known variant

Reference ID: rs121434640

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.874	1
	4.531	1
(flanking)	1.33	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	19934	wt: 0.8419 / mu: 0.9148 (marginal change - not scored)	wt: GCGCCAGGTTAGAGG mu: GCACCAGGTTAGAGG	GCCA\|ggtt
Donor marginally increased	19936	wt: 0.4054 / mu: 0.4390 (marginal change - not scored)	wt: GCCAGGTTAGAGGGA mu: ACCAGGTTAGAGGGA	CAGG\|ttag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

273

mutated

not conserved

273

Ptroglodytes

all identical

ENSPTRG00000003558

273

Mmulatta

all identical

ENSMMUG00000022964

273

Fcatus

all identical

ENSFCAG00000002526

273

Mmusculus

all identical

ENSMUSG00000002109

273

Ggallus

all identical

ENSGALG00000008218

293

Trubripes

no homologue

Drerio

all identical

ENSDARG00000041140

282

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000003980

282

protein features

start (aa)	end (aa)	feature	details
240	280	REPEAT	WD 3.	lost
256	274	MOTIF	DWD box.	lost
272	274	TURN		lost
273	273	MUTAGEN	R->A: Impairs interaction with DDB1.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1284 / 1284

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

428 / 428

position of stopcodon in wt / mu cDNA

1479 / 1479

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

196 / 196

chromosome

strand

last intron/exon boundary

1430

theoretical NMD boundary in CDS

1184

length of CDS

1284

coding sequence (CDS) position

818

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

1013

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

19931

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

47256423

original gDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered gDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

original cDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered cDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

wildtype AA sequence

MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQGL QQSFLHTLDS YRILQKAAPF DRRATSLAWH
PTHPSTVAVG SKGGDIMLWN FGIKDKPTFI KGIGAGGSIT GLKFNPLNTN QFYASSMEGT
TRLQDFKGNI LRVFASSDTI NIWFCSLDVS ASSRMVVTGD NVGNVILLNM DGKELWNLRM
HKKKVTHVAL NPCCDWFLAT ASVDQTVKIW DLRQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*

mutated AA sequence

MAPKKRPETQ KTSEIVLRPR NKRSRSPLEL EPEAKKLCAK GSGPSRRCDS DCLWVGLAGP
QILPPCRSIV RTLHQHKLGR ASWPSVQQGL QQSFLHTLDS YRILQKAAPF DRRATSLAWH
PTHPSTVAVG SKGGDIMLWN FGIKDKPTFI KGIGAGGSIT GLKFNPLNTN QFYASSMEGT
TRLQDFKGNI LRVFASSDTI NIWFCSLDVS ASSRMVVTGD NVGNVILLNM DGKELWNLRM
HKKKVTHVAL NPCCDWFLAT ASVDQTVKIW DLHQVRGKAS FLYSLPHRHP VNAACFSPDG
ARLLTTDQKS EIRVYSASQW DCPLGLIPHP HRHFQHLTPI KAAWHPRYNL IVVGRYPDPN
FKSCTPYELR TIDVFDGNSG KMMCQLYDPE SSGISSLNEF NPMGDTLASA MGYHILIWSQ
EEARTRK*

speed

0.96 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960485)
known disease mutation: rs8788 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256423G>AN/A show variant in all transcripts IGV

HGNC symbol

DDB2

Ensembl transcript ID

ENST00000378600

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.19931G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434640

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.874	1
	4.531	1
(flanking)	1.33	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	19934	wt: 0.8419 / mu: 0.9148 (marginal change - not scored)	wt: GCGCCAGGTTAGAGG mu: GCACCAGGTTAGAGG	GCCA\|ggtt
Donor marginally increased	19936	wt: 0.4054 / mu: 0.4390 (marginal change - not scored)	wt: GCCAGGTTAGAGGGA mu: ACCAGGTTAGAGGGA	CAGG\|ttag

distance from splice site

2965

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

196 / 196

chromosome

strand

last intron/exon boundary

863

theoretical NMD boundary in CDS

617

length of CDS

717

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)

19931

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

47256423

original gDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered gDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

1.04 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM960485)
known disease mutation: rs8788 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:47256423G>AN/A show variant in all transcripts IGV

HGNC symbol

DDB2

Ensembl transcript ID

ENST00000378601

Genbank transcript ID

N/A

UniProt peptide

N/A

alteration type

single base exchange

alteration region

intron

DNA changes

g.19931G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs121434640

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	2	2

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.874	1
	4.531	1
(flanking)	1.33	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	19934	wt: 0.8419 / mu: 0.9148 (marginal change - not scored)	wt: GCGCCAGGTTAGAGG mu: GCACCAGGTTAGAGG	GCCA\|ggtt
Donor marginally increased	19936	wt: 0.4054 / mu: 0.4390 (marginal change - not scored)	wt: GCCAGGTTAGAGGGA mu: ACCAGGTTAGAGGGA	CAGG\|ttag

distance from splice site

200

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

N/A

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

196 / 196

chromosome

strand

last intron/exon boundary

1252

theoretical NMD boundary in CDS

1006

length of CDS

735

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)

19931

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

47256423

original gDNA sequence snippet

AGTGAAAATTTGGGACCTGCGCCAGGTTAGAGGGAAAGCCA

altered gDNA sequence snippet

AGTGAAAATTTGGGACCTGCACCAGGTTAGAGGGAAAGCCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

mutated AA sequence

N/A

speed

1.09 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems