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: ENST00000382848
Querying Taster for transcript #2: ENST00000382844
MT speed 1.62 s - this script 3.635033 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJB2	disease_causing	0.999999876624911	simple_aae		affected		M163V	single base exchange	rs80338949		show file
GJB2	disease_causing	0.999999876624911	simple_aae		affected		M163V	single base exchange	rs80338949		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999876624911 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CI024277)
known disease mutation at this position (HGMD CM013725)
known disease mutation at this position (HGMD CM035027)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20763234T>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.487A>G
cDNA.625A>G
g.3804A>G

AA changes

M163V Score: 21 explain score(s)

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

163

frameshift

known variant

Reference ID: rs80338949

database	homozygous (C/C)	heterozygous	allele carriers
1000G	0	2	2
ExAC	0	20	20

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035027)

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035027)
known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035027)
known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)

known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035027)
known disease mutation at this position, please check HGMD for details (HGMD ID CI024277)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013725)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035027)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.085	1
	5.085	1
(flanking)	0.47	0.978

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 gained	3803	0.75	mu: TTCTCCGTGCAGCGG	CTCC\|gtgc

distance from splice site

509

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

all conserved

163

Ptroglodytes

all identical

ENSPTRG00000031248

163

Mmulatta

all identical

ENSMMUG00000010522

163

Fcatus

all identical

ENSFCAG00000006961

163

Mmusculus

all identical

ENSMUSG00000046352

163

Ggallus

all identical

ENSGALG00000017136

163

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

162

protein features

start (aa)	end (aa)	feature	details
155	192	TOPO_DOM	Extracellular (Potential).	lost
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

487

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

625

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

3804

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

20763234

original gDNA sequence snippet

TCATGTACGACGGCTTCTCCATGCAGCGGCTGGTGAAGTGC

altered gDNA sequence snippet

TCATGTACGACGGCTTCTCCGTGCAGCGGCTGGTGAAGTGC

original cDNA sequence snippet

TCATGTACGACGGCTTCTCCATGCAGCGGCTGGTGAAGTGC

altered cDNA sequence snippet

TCATGTACGACGGCTTCTCCGTGCAGCGGCTGGTGAAGTGC

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 IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSVQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*

speed

0.83 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: 0.999999876624911 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CI024277)
known disease mutation at this position (HGMD CM013725)
known disease mutation at this position (HGMD CM035027)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20763234T>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.487A>G
cDNA.686A>G
g.3804A>G

AA changes

M163V Score: 21 explain score(s)

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

163

frameshift

known variant

Reference ID: rs80338949

database	homozygous (C/C)	heterozygous	allele carriers
1000G	0	2	2
ExAC	0	20	20

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.085	1
	5.085	1
(flanking)	0.47	0.978

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 gained	3803	0.75	mu: TTCTCCGTGCAGCGG	CTCC\|gtgc

distance from splice site

686

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

163

mutated

all conserved

163

Ptroglodytes

all identical

ENSPTRG00000031248

163

Mmulatta

all identical

ENSMMUG00000010522

163

Fcatus

all identical

ENSFCAG00000006961

163

Mmusculus

all identical

ENSMUSG00000046352

163

Ggallus

all identical

ENSGALG00000017136

163

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

165

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

162

protein features

start (aa)	end (aa)	feature	details
155	192	TOPO_DOM	Extracellular (Potential).	lost
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

487

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

686

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

3804

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

20763234

original gDNA sequence snippet

TCATGTACGACGGCTTCTCCATGCAGCGGCTGGTGAAGTGC

altered gDNA sequence snippet

TCATGTACGACGGCTTCTCCGTGCAGCGGCTGGTGAAGTGC

original cDNA sequence snippet

TCATGTACGACGGCTTCTCCATGCAGCGGCTGGTGAAGTGC

altered cDNA sequence snippet

TCATGTACGACGGCTTCTCCGTGCAGCGGCTGGTGAAGTGC

wildtype AA sequence

mutated AA sequence

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

speed

0.79 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems