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: ENST00000382848
Querying Taster for transcript #2: ENST00000382844
MT speed 2.57 s - this script 4.541178 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJB2	polymorphism	1.67899028014062e-12	simple_aae		affected		S113R	single base exchange	rs80338946		show file
GJB2	polymorphism	1.67899028014062e-12	simple_aae		affected		S113R	single base exchange	rs80338946		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999998321 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980928)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20763382A>CN/A show variant in all transcripts IGV

HGNC symbol

GJB2

Ensembl transcript ID

ENST00000382848

Genbank transcript ID

NM_004004

UniProt peptide

P29033

alteration type

single base exchange

alteration region

CDS

DNA changes

c.339T>G
cDNA.477T>G
g.3656T>G

AA changes

S113R Score: 110 explain score(s)

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

113

frameshift

known variant

Reference ID: rs80338946

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation at this position, please check HGMD for details (HGMD ID CM980928)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980928)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980928)

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.273	0.154
	-0.404	0.001
(flanking)	-3.471	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
Donor increased	3647	wt: 0.58 / mu: 0.67	wt: GGGGAGATAAAGAGT mu: GGGGAGATAAAGAGG	GGAG\|ataa
Donor gained	3655	0.43	mu: AAAGAGGGAATTTAA	AGAG\|ggaa

distance from splice site

361

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

113

mutated

not conserved

113

Ptroglodytes

all identical

ENSPTRG00000031248

113

Mmulatta

all conserved

ENSMMUG00000010522

113

Fcatus

all conserved

ENSFCAG00000006961

113

Mmusculus

all conserved

ENSMUSG00000046352

113

Ggallus

not conserved

ENSGALG00000017136

113

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000042707

113

KGD

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026112

113

FGG

protein features

start (aa)	end (aa)	feature	details
99	131	TOPO_DOM	Cytoplasmic (Potential).	lost
112	112	CONFLICT	K -> N (in Ref. 4; AAY25170).	might get lost (downstream of altered splice site)
126	130	TURN		might get lost (downstream of altered splice site)
131	156	HELIX		might get lost (downstream of altered splice site)
132	154	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
155	192	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
157	159	TURN		might get lost (downstream of altered splice site)
160	162	STRAND		might get lost (downstream of altered splice site)
165	169	STRAND		might get lost (downstream of altered splice site)
169	169	DISULFID		might get lost (downstream of altered splice site)
174	174	DISULFID		might get lost (downstream of altered splice site)
174	181	STRAND		might get lost (downstream of altered splice site)
180	180	DISULFID		might get lost (downstream of altered splice site)
185	215	HELIX		might get lost (downstream of altered splice site)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	226	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

681 / 681

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

227 / 227

position of stopcodon in wt / mu cDNA

819 / 819

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

139 / 139

chromosome

strand

-1

last intron/exon boundary

117

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

681

coding sequence (CDS) position

339

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

477

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

3656

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

20763382

original gDNA sequence snippet

ATCAAGGGGGAGATAAAGAGTGAATTTAAGGACATCGAGGA

altered gDNA sequence snippet

ATCAAGGGGGAGATAAAGAGGGAATTTAAGGACATCGAGGA

original cDNA sequence snippet

ATCAAGGGGGAGATAAAGAGTGAATTTAAGGACATCGAGGA

altered cDNA sequence snippet

ATCAAGGGGGAGATAAAGAGGGAATTTAAGGACATCGAGGA

wildtype AA sequence

MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*

mutated AA sequence

MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKREFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*

speed

1.29 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: 0.999999999998321 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980928)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20763382A>CN/A show variant in all transcripts IGV

HGNC symbol

GJB2

Ensembl transcript ID

ENST00000382844

Genbank transcript ID

N/A

UniProt peptide

P29033

alteration type

single base exchange

alteration region

CDS

DNA changes

c.339T>G
cDNA.538T>G
g.3656T>G

AA changes

S113R Score: 110 explain score(s)

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

113

frameshift

known variant

Reference ID: rs80338946

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.273	0.154
	-0.404	0.001
(flanking)	-3.471	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
Donor increased	3647	wt: 0.58 / mu: 0.67	wt: GGGGAGATAAAGAGT mu: GGGGAGATAAAGAGG	GGAG\|ataa
Donor gained	3655	0.43	mu: AAAGAGGGAATTTAA	AGAG\|ggaa

distance from splice site

538

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

113

mutated

not conserved

113

Ptroglodytes

all identical

ENSPTRG00000031248

113

Mmulatta

all conserved

ENSMMUG00000010522

113

Fcatus

all conserved

ENSFCAG00000006961

113

Mmusculus

all conserved

ENSMUSG00000046352

113

Ggallus

not conserved

ENSGALG00000017136

113

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000042707

113

KGD

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000026112

113

FGG

protein features

start (aa)	end (aa)	feature	details
99	131	TOPO_DOM	Cytoplasmic (Potential).	lost
112	112	CONFLICT	K -> N (in Ref. 4; AAY25170).	might get lost (downstream of altered splice site)
126	130	TURN		might get lost (downstream of altered splice site)
131	156	HELIX		might get lost (downstream of altered splice site)
132	154	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
155	192	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
157	159	TURN		might get lost (downstream of altered splice site)
160	162	STRAND		might get lost (downstream of altered splice site)
165	169	STRAND		might get lost (downstream of altered splice site)
169	169	DISULFID		might get lost (downstream of altered splice site)
174	174	DISULFID		might get lost (downstream of altered splice site)
174	181	STRAND		might get lost (downstream of altered splice site)
180	180	DISULFID		might get lost (downstream of altered splice site)
185	215	HELIX		might get lost (downstream of altered splice site)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	226	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

681 / 681

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

227 / 227

position of stopcodon in wt / mu cDNA

880 / 880

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

200 / 200

chromosome

strand

-1

last intron/exon boundary

theoretical NMD boundary in CDS

cannot be calculated, too little distance between start ATG and last intron/exon boundary

length of CDS

681

coding sequence (CDS) position

339

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

538

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

3656

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

20763382

original gDNA sequence snippet

ATCAAGGGGGAGATAAAGAGTGAATTTAAGGACATCGAGGA

altered gDNA sequence snippet

ATCAAGGGGGAGATAAAGAGGGAATTTAAGGACATCGAGGA

original cDNA sequence snippet

ATCAAGGGGGAGATAAAGAGTGAATTTAAGGACATCGAGGA

altered cDNA sequence snippet

ATCAAGGGGGAGATAAAGAGGGAATTTAAGGACATCGAGGA

wildtype AA sequence

mutated AA sequence

speed

1.28 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems