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: ENST00000241124
Querying Taster for transcript #2: ENST00000400065
Querying Taster for transcript #3: ENST00000400066
Querying Taster for transcript #4: ENST00000356192
MT speed 0 s - this script 4.378858 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
GJB6	disease_causing_automatic	0.999999886947596	simple_aae		affected	0	V37E	single base exchange	rs104894416		show file
GJB6	disease_causing_automatic	0.999999886947596	simple_aae		affected	0	V37E	single base exchange	rs104894416		show file
GJB6	disease_causing_automatic	0.999999886947596	simple_aae		affected	0	V37E	single base exchange	rs104894416		show file
GJB6	disease_causing_automatic	0.999999886947596	simple_aae		affected	0	V37E	single base exchange	rs104894416		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999886947596 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020718)
known disease mutation: rs5547 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20797510A>TN/A show variant in all transcripts IGV

HGNC symbol

GJB6

Ensembl transcript ID

ENST00000241124

Genbank transcript ID

NM_006783

UniProt peptide

O95452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>A
cDNA.408T>A
g.9025T>A

AA changes

V37E Score: 121 explain score(s)

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

frameshift

known variant

Reference ID: rs104894416
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5547 (pathogenic for Hidrotic ectodermal dysplasia syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM020718)

known disease mutation at this position, please check HGMD for details (HGMD ID CM020718)
known disease mutation at this position, please check HGMD for details (HGMD ID CM020718)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1	0.303
	4.987	0.995
(flanking)	4.377	0.995

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
Acc marginally increased	9018	wt: 0.5447 / mu: 0.5774 (marginal change - not scored)	wt: TCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAG mu: TCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAG	atga\|TCCT
Acc marginally increased	9016	wt: 0.8642 / mu: 0.8644 (marginal change - not scored)	wt: CATCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCC mu: CATCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCC	tcat\|GATC
Acc marginally increased	9025	wt: 0.4021 / mu: 0.4341 (marginal change - not scored)	wt: TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT mu: TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT	tcgt\|GGTG
Donor gained	9020	0.40	mu: ATGATCCTCGAGGTG	GATC\|ctcg
Donor gained	9021	0.56	mu: TGATCCTCGAGGTGG	ATCC\|tcga

distance from splice site

125

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005683

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040055

Ggallus

all identical

ENSGALG00000017136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

protein features

start (aa)	end (aa)	feature	details
23	45	TRANSMEM	Helical; (Potential).	lost
46	75	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
76	98	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
99	131	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
124	124	CONFLICT	Q -> H (in Ref. 1; CAA06611).	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)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	261	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

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

1084 / 1084

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

299 / 299

chromosome

strand

-1

last intron/exon boundary

284

theoretical NMD boundary in CDS

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

length of CDS

786

coding sequence (CDS) position

110

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

408

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

9025

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

20797510

original gDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered gDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

original cDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered cDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

wildtype AA sequence

MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*

mutated AA sequence

MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILEVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*

speed

0.55 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: 0.999999886947596 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020718)
known disease mutation: rs5547 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20797510A>TN/A show variant in all transcripts IGV

HGNC symbol

GJB6

Ensembl transcript ID

ENST00000400065

Genbank transcript ID

NM_001110221

UniProt peptide

O95452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>A
cDNA.405T>A
g.9025T>A

AA changes

V37E Score: 121 explain score(s)

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

frameshift

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1	0.303
	4.987	0.995
(flanking)	4.377	0.995

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
Acc marginally increased	9018	wt: 0.5447 / mu: 0.5774 (marginal change - not scored)	wt: TCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAG mu: TCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAG	atga\|TCCT
Acc marginally increased	9016	wt: 0.8642 / mu: 0.8644 (marginal change - not scored)	wt: CATCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCC mu: CATCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCC	tcat\|GATC
Acc marginally increased	9025	wt: 0.4021 / mu: 0.4341 (marginal change - not scored)	wt: TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT mu: TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT	tcgt\|GGTG
Donor gained	9020	0.40	mu: ATGATCCTCGAGGTG	GATC\|ctcg
Donor gained	9021	0.56	mu: TGATCCTCGAGGTGG	ATCC\|tcga

distance from splice site

125

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005683

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040055

Ggallus

all identical

ENSGALG00000017136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

protein features

start (aa)	end (aa)	feature	details
23	45	TRANSMEM	Helical; (Potential).	lost
46	75	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
76	98	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
99	131	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
124	124	CONFLICT	Q -> H (in Ref. 1; CAA06611).	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)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	261	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

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

1081 / 1081

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

296 / 296

chromosome

strand

-1

last intron/exon boundary

281

theoretical NMD boundary in CDS

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

length of CDS

786

coding sequence (CDS) position

110

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

405

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

9025

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

20797510

original gDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered gDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

original cDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered cDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

wildtype AA sequence

mutated AA sequence

speed

1.28 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999886947596 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020718)
known disease mutation: rs5547 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20797510A>TN/A show variant in all transcripts IGV

HGNC symbol

GJB6

Ensembl transcript ID

ENST00000400066

Genbank transcript ID

NM_001110220

UniProt peptide

O95452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>A
cDNA.527T>A
g.9025T>A

AA changes

V37E Score: 121 explain score(s)

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

frameshift

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1	0.303
	4.987	0.995
(flanking)	4.377	0.995

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
Acc marginally increased	9018	wt: 0.5447 / mu: 0.5774 (marginal change - not scored)	wt: TCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAG mu: TCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAG	atga\|TCCT
Acc marginally increased	9016	wt: 0.8642 / mu: 0.8644 (marginal change - not scored)	wt: CATCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCC mu: CATCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCC	tcat\|GATC
Acc marginally increased	9025	wt: 0.4021 / mu: 0.4341 (marginal change - not scored)	wt: TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT mu: TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT	tcgt\|GGTG
Donor gained	9020	0.40	mu: ATGATCCTCGAGGTG	GATC\|ctcg
Donor gained	9021	0.56	mu: TGATCCTCGAGGTGG	ATCC\|tcga

distance from splice site

125

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005683

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040055

Ggallus

all identical

ENSGALG00000017136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

protein features

start (aa)	end (aa)	feature	details
23	45	TRANSMEM	Helical; (Potential).	lost
46	75	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
76	98	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
99	131	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
124	124	CONFLICT	Q -> H (in Ref. 1; CAA06611).	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)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	261	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

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

1203 / 1203

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

418 / 418

chromosome

strand

-1

last intron/exon boundary

403

theoretical NMD boundary in CDS

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

length of CDS

786

coding sequence (CDS) position

110

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

527

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

9025

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

20797510

original gDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered gDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

original cDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered cDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

wildtype AA sequence

mutated AA sequence

speed

0.45 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999886947596 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM020718)
known disease mutation: rs5547 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr13:20797510A>TN/A show variant in all transcripts IGV

HGNC symbol

GJB6

Ensembl transcript ID

ENST00000356192

Genbank transcript ID

NM_001110219

UniProt peptide

O95452

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110T>A
cDNA.731T>A
g.9025T>A

AA changes

V37E Score: 121 explain score(s)

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

frameshift

known variant

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1	0.303
	4.987	0.995
(flanking)	4.377	0.995

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
Acc marginally increased	9018	wt: 0.5447 / mu: 0.5774 (marginal change - not scored)	wt: TCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAG mu: TCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAG	atga\|TCCT
Acc marginally increased	9016	wt: 0.8642 / mu: 0.8644 (marginal change - not scored)	wt: CATCTTTATTTTCCGAGTCATGATCCTCGTGGTGGCTGCCC mu: CATCTTTATTTTCCGAGTCATGATCCTCGAGGTGGCTGCCC	tcat\|GATC
Acc marginally increased	9025	wt: 0.4021 / mu: 0.4341 (marginal change - not scored)	wt: TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT mu: TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT	tcgt\|GGTG
Donor gained	9020	0.40	mu: ATGATCCTCGAGGTG	GATC\|ctcg
Donor gained	9021	0.56	mu: TGATCCTCGAGGTGG	ATCC\|tcga

distance from splice site

125

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000005683

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000040055

Ggallus

all identical

ENSGALG00000017136

Trubripes

no homologue

Drerio

all identical

ENSDARG00000042707

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000026112

protein features

start (aa)	end (aa)	feature	details
23	45	TRANSMEM	Helical; (Potential).	lost
46	75	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
76	98	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
99	131	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
124	124	CONFLICT	Q -> H (in Ref. 1; CAA06611).	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)
193	215	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
216	261	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

786 / 786

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

262 / 262

position of stopcodon in wt / mu cDNA

1407 / 1407

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

622 / 622

chromosome

strand

-1

last intron/exon boundary

607

theoretical NMD boundary in CDS

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

length of CDS

786

coding sequence (CDS) position

110

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

731

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

9025

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

20797510

original gDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered gDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

original cDNA sequence snippet

TTTCCGAGTCATGATCCTCGTGGTGGCTGCCCAGGAAGTGT

altered cDNA sequence snippet

TTTCCGAGTCATGATCCTCGAGGTGGCTGCCCAGGAAGTGT

wildtype AA sequence

mutated AA sequence

speed

0.47 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