MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 4 transcript(s)...
Querying Taster for transcript #1: ENST00000246554
Querying Taster for transcript #2: ENST00000592141
Querying Taster for transcript #3: ENST00000392201
Querying Taster for transcript #4: ENST00000590618
MT speed 0 s - this script 4.09415 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COX6B1	disease_causing_automatic	0.99998679943329	simple_aae		affected	0	R16H	single base exchange	rs121909602		show file
COX6B1	disease_causing_automatic	0.999999967441827	simple_aae		affected	0	R20H	single base exchange	rs121909602		show file
COX6B1	disease_causing_automatic	0.999999967441827	simple_aae		affected	0	R32H	single base exchange	rs121909602		show file
COX6B1	disease_causing_automatic	0.999999967441827	simple_aae		affected	0	R37H	single base exchange	rs121909602		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99998679943329 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082579)
known disease mutation: rs16875 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:36142204G>AN/A show variant in all transcripts IGV

HGNC symbol

COX6B1

Ensembl transcript ID

ENST00000590618

Genbank transcript ID

N/A

UniProt peptide

P14854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.47G>A
cDNA.58G>A
g.3080G>A

AA changes

R16H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs121909602

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

known disease mutation: rs16875 (pathogenic for Mitochondrial complex IV deficiency) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082579)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082579)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082579)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.17	1
	4.96	1
(flanking)	0.888	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 increased	3076	wt: 0.58 / mu: 0.98	wt: TTGACAGCCGCTTCC mu: TTGACAGCCACTTCC	GACA\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010854

Mmulatta

all identical

ENSMMUG00000016765

Fcatus

all identical

ENSFCAG00000006378

Mmusculus

all identical

ENSMUSG00000036751

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016356

Drerio

all identical

ENSDARG00000045230

Dmelanogaster

no alignment

FBgn0031066

n/a

Celegans

no alignment

Y71H2AM.5

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	30	DISULFID	By similarity.	might get lost (downstream of altered splice site)
40	40	DISULFID	By similarity.	might get lost (downstream of altered splice site)
54	54	DISULFID	By similarity.	might get lost (downstream of altered splice site)
65	65	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

111 / 111

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

37 / 37

position of stopcodon in wt / mu cDNA

122 / 122

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

12 / 12

chromosome

strand

last intron/exon boundary

106

theoretical NMD boundary in CDS

length of CDS

111

coding sequence (CDS) position

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

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

3080

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

36142204

original gDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered gDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

original cDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered cDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

wildtype AA sequence

METKIKNYKT APFDSRFPNQ NQTRNCWQNY LGHRLG*

mutated AA sequence

METKIKNYKT APFDSHFPNQ NQTRNCWQNY LGHRLG*

speed

0.56 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: 0.999999967441827 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082579)
known disease mutation: rs16875 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:36142204G>AN/A show variant in all transcripts IGV

HGNC symbol

COX6B1

Ensembl transcript ID

ENST00000246554

Genbank transcript ID

NM_001863

UniProt peptide

P14854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.59G>A
cDNA.251G>A
g.3080G>A

AA changes

R20H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs121909602

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.17	1
	4.96	1
(flanking)	0.888	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 increased	3076	wt: 0.58 / mu: 0.98	wt: TTGACAGCCGCTTCC mu: TTGACAGCCACTTCC	GACA\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010854

Mmulatta

all identical

ENSMMUG00000016765

Fcatus

all identical

ENSFCAG00000006378

Mmusculus

all identical

ENSMUSG00000036751

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016356

Drerio

all identical

ENSDARG00000045230

Dmelanogaster

all identical

FBgn0031066

Celegans

all identical

Y71H2AM.5

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	30	DISULFID	By similarity.	might get lost (downstream of altered splice site)
40	40	DISULFID	By similarity.	might get lost (downstream of altered splice site)
54	54	DISULFID	By similarity.	might get lost (downstream of altered splice site)
65	65	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

261 / 261

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

87 / 87

position of stopcodon in wt / mu cDNA

453 / 453

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

193 / 193

chromosome

strand

last intron/exon boundary

400

theoretical NMD boundary in CDS

157

length of CDS

261

coding sequence (CDS) position

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

251

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

3080

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

36142204

original gDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered gDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

original cDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered cDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

wildtype AA sequence

MAEDMETKIK NYKTAPFDSR FPNQNQTRNC WQNYLDFHRC QKAMTAKGGD ISVCEWYQRV
YQSLCPTSWV TDWDEQRAEG TFPGKI*

mutated AA sequence

MAEDMETKIK NYKTAPFDSH FPNQNQTRNC WQNYLDFHRC QKAMTAKGGD ISVCEWYQRV
YQSLCPTSWV TDWDEQRAEG TFPGKI*

speed

0.67 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999967441827 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082579)
known disease mutation: rs16875 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:36142204G>AN/A show variant in all transcripts IGV

HGNC symbol

COX6B1

Ensembl transcript ID

ENST00000592141

Genbank transcript ID

N/A

UniProt peptide

P14854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.95G>A
cDNA.324G>A
g.3080G>A

AA changes

R32H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs121909602

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.17	1
	4.96	1
(flanking)	0.888	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 increased	3076	wt: 0.58 / mu: 0.98	wt: TTGACAGCCGCTTCC mu: TTGACAGCCACTTCC	GACA\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010854

Mmulatta

all identical

ENSMMUG00000016765

Fcatus

all identical

ENSFCAG00000006378

Mmusculus

all identical

ENSMUSG00000036751

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016356

Drerio

all identical

ENSDARG00000045230

Dmelanogaster

all identical

FBgn0031066

Celegans

all identical

Y71H2AM.5

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
30	30	DISULFID	By similarity.	might get lost (downstream of altered splice site)
40	40	DISULFID	By similarity.	might get lost (downstream of altered splice site)
54	54	DISULFID	By similarity.	might get lost (downstream of altered splice site)
65	65	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

297 / 297

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

99 / 99

position of stopcodon in wt / mu cDNA

526 / 526

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

230 / 230

chromosome

strand

last intron/exon boundary

473

theoretical NMD boundary in CDS

193

length of CDS

297

coding sequence (CDS) position

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

324

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

3080

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

36142204

original gDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered gDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

original cDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered cDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

wildtype AA sequence

MHPHPQIPGF STMAEDMETK IKNYKTAPFD SRFPNQNQTR NCWQNYLDFH RCQKAMTAKG
GDISVCEWYQ RVYQSLCPTS WVTDWDEQRA EGTFPGKI*

mutated AA sequence

MHPHPQIPGF STMAEDMETK IKNYKTAPFD SHFPNQNQTR NCWQNYLDFH RCQKAMTAKG
GDISVCEWYQ RVYQSLCPTS WVTDWDEQRA EGTFPGKI*

speed

0.67 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999967441827 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082579)
known disease mutation: rs16875 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:36142204G>AN/A show variant in all transcripts IGV

HGNC symbol

COX6B1

Ensembl transcript ID

ENST00000392201

Genbank transcript ID

N/A

UniProt peptide

P14854

alteration type

single base exchange

alteration region

CDS

DNA changes

c.110G>A
cDNA.154G>A
g.3080G>A

AA changes

R37H Score: 29 explain score(s)

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

frameshift

known variant

Reference ID: rs121909602

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.17	1
	4.96	1
(flanking)	0.888	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 increased	3076	wt: 0.58 / mu: 0.98	wt: TTGACAGCCGCTTCC mu: TTGACAGCCACTTCC	GACA\|gccg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000010854

Mmulatta

all identical

ENSMMUG00000016765

Fcatus

all identical

ENSFCAG00000006378

Mmusculus

all identical

ENSMUSG00000036751

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000016356

Drerio

all identical

ENSDARG00000045230

Dmelanogaster

all identical

FBgn0031066

Celegans

all identical

Y71H2AM.5

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
40	40	DISULFID	By similarity.	might get lost (downstream of altered splice site)
54	54	DISULFID	By similarity.	might get lost (downstream of altered splice site)
65	65	DISULFID	By similarity.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

312 / 312

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

104 / 104

position of stopcodon in wt / mu cDNA

356 / 356

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

45 / 45

chromosome

strand

last intron/exon boundary

303

theoretical NMD boundary in CDS

208

length of CDS

312

coding sequence (CDS) position

110

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

154

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

3080

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

36142204

original gDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered gDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

original cDNA sequence snippet

GACCGCCCCTTTTGACAGCCGCTTCCCCAACCAGAACCAGA

altered cDNA sequence snippet

GACCGCCCCTTTTGACAGCCACTTCCCCAACCAGAACCAGA

wildtype AA sequence

MHPHPQIPGR DLAGFSTMAE DMETKIKNYK TAPFDSRFPN QNQTRNCWQN YLDFHRCQKA
MTAKGGDISV CEWYQRVYQS LCPTSWVTDW DEQRAEGTFP GKI*

mutated AA sequence

MHPHPQIPGR DLAGFSTMAE DMETKIKNYK TAPFDSHFPN QNQTRNCWQN YLDFHRCQKA
MTAKGGDISV CEWYQRVYQS LCPTSWVTDW DEQRAEGTFP GKI*

speed

0.79 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