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: ENST00000370483
Querying Taster for transcript #2: ENST00000016171
MT speed 1.92 s - this script 3.957431 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COX15	disease_causing_automatic	0.999999987319689	simple_aae		affected	0	R217W	single base exchange	rs28939711		show file
COX15	disease_causing_automatic	0.999999987319689	simple_aae		affected	0	R217W	single base exchange	rs28939711		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999987319689 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030209)
known disease mutation: rs6175 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:101483814G>AN/A show variant in all transcripts IGV

HGNC symbol

COX15

Ensembl transcript ID

ENST00000370483

Genbank transcript ID

NM_004376

UniProt peptide

Q7KZN9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.649C>T
cDNA.700C>T
g.8053C>T

AA changes

R217W Score: 101 explain score(s)

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

217

frameshift

known variant

Reference ID: rs28939711

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

known disease mutation: rs6175 (pathogenic for Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiency 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030209)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030209)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030209)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.307	1
	3.583	1
(flanking)	1.16	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
Acc increased	8055	wt: 0.52 / mu: 0.63	wt: GACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTTGC mu: GACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTTGC	tcgg\|GTCA
Acc increased	8063	wt: 0.67 / mu: 0.77	wt: TGACATCCCTCGGGTCAGTCAGTACCGCCTTGCTGCCCACC mu: TGACATCCCTTGGGTCAGTCAGTACCGCCTTGCTGCCCACC	gtca\|GTAC
Acc marginally increased	8053	wt: 0.2259 / mu: 0.2280 (marginal change - not scored)	wt: CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT mu: CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT	cctc\|GGGT
Acc gained	8059	0.32	mu: CCCATGACATCCCTTGGGTCAGTCAGTACCGCCTTGCTGCC	gtca\|GTCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000002835

217

Mmulatta

all identical

ENSMMUG00000023762

219

Fcatus

not conserved

ENSFCAG00000014378

220

Mmusculus

all identical

ENSMUSG00000040018

220

Ggallus

all identical

ENSGALG00000007465

163

Trubripes

no homologue

Drerio

all identical

ENSDARG00000075933

206

Dmelanogaster

all identical

FBgn0034938

195

Celegans

all identical

T06D8.5

201

Xtropicalis

all identical

ENSXETG00000003745

218

protein features

start (aa)	end (aa)	feature	details
227	247	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
269	289	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
324	344	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
357	377	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
382	402	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1167 / 1167

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

389 / 389

position of stopcodon in wt / mu cDNA

1218 / 1218

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

52 / 52

chromosome

strand

-1

last intron/exon boundary

1153

theoretical NMD boundary in CDS

1051

length of CDS

1167

coding sequence (CDS) position

649

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

700

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

8053

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

101483814

original gDNA sequence snippet

CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT

altered gDNA sequence snippet

CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT

original cDNA sequence snippet

CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT

altered cDNA sequence snippet

CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT

wildtype AA sequence

MQRLLFPPLR ALKGRQYLPL LAPRAAPRAQ CDCIRRPLRP GQYSTISEVA LQSGRGTVSL
PSKAAERVVG RWLLVCSGTV AGAVILGGVT RLTESGLSMV DWHLIKEMKP PTSQEEWEAE
FQRYQQFPEF KILNHDMTLT EFKFIWYMEY SHRMWGRLVG LVYILPAAYF WRKGWLSRGM
KGRVLALCGL VCFQGLLGWY MVKSGLEEKS DSHDIPRVSQ YRLAAHLGSA LVLYCASLWT
SLSLLLPPHK LPETHQLLQL RRFAHGTAGL VFLTALSGAF VAGLDAGLVY NSFPKMGESW
IPEDLFTFSP ILRNVFENPT MVQFDHRILG ITSVTAITVL YFLSRRIPLP RRTKMAAVTL
LALAYTQGPV LFNFTFKISD LDEGIRNI*

mutated AA sequence

MQRLLFPPLR ALKGRQYLPL LAPRAAPRAQ CDCIRRPLRP GQYSTISEVA LQSGRGTVSL
PSKAAERVVG RWLLVCSGTV AGAVILGGVT RLTESGLSMV DWHLIKEMKP PTSQEEWEAE
FQRYQQFPEF KILNHDMTLT EFKFIWYMEY SHRMWGRLVG LVYILPAAYF WRKGWLSRGM
KGRVLALCGL VCFQGLLGWY MVKSGLEEKS DSHDIPWVSQ YRLAAHLGSA LVLYCASLWT
SLSLLLPPHK LPETHQLLQL RRFAHGTAGL VFLTALSGAF VAGLDAGLVY NSFPKMGESW
IPEDLFTFSP ILRNVFENPT MVQFDHRILG ITSVTAITVL YFLSRRIPLP RRTKMAAVTL
LALAYTQGPV LFNFTFKISD LDEGIRNI*

speed

0.97 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: 0.999999987319689 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM030209)
known disease mutation: rs6175 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:101483814G>AN/A show variant in all transcripts IGV

HGNC symbol

COX15

Ensembl transcript ID

ENST00000016171

Genbank transcript ID

NM_078470

UniProt peptide

Q7KZN9

alteration type

single base exchange

alteration region

CDS

DNA changes

c.649C>T
cDNA.700C>T
g.8053C>T

AA changes

R217W Score: 101 explain score(s)

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

217

frameshift

known variant

Reference ID: rs28939711

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

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.307	1
	3.583	1
(flanking)	1.16	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
Acc increased	8055	wt: 0.52 / mu: 0.63	wt: GACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTTGC mu: GACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTTGC	tcgg\|GTCA
Acc increased	8063	wt: 0.67 / mu: 0.77	wt: TGACATCCCTCGGGTCAGTCAGTACCGCCTTGCTGCCCACC mu: TGACATCCCTTGGGTCAGTCAGTACCGCCTTGCTGCCCACC	gtca\|GTAC
Acc marginally increased	8053	wt: 0.2259 / mu: 0.2280 (marginal change - not scored)	wt: CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT mu: CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT	cctc\|GGGT
Acc gained	8059	0.32	mu: CCCATGACATCCCTTGGGTCAGTCAGTACCGCCTTGCTGCC	gtca\|GTCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

217

mutated

not conserved

217

Ptroglodytes

all identical

ENSPTRG00000002835

217

Mmulatta

all identical

ENSMMUG00000023762

219

Fcatus

not conserved

ENSFCAG00000014378

220

Mmusculus

all identical

ENSMUSG00000040018

220

Ggallus

all identical

ENSGALG00000007465

163

Trubripes

no homologue

Drerio

all identical

ENSDARG00000075933

206

Dmelanogaster

all identical

FBgn0034938

195

Celegans

all identical

T06D8.5

201

Xtropicalis

all identical

ENSXETG00000003745

218

protein features

start (aa)	end (aa)	feature	details
227	247	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
269	289	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
324	344	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
357	377	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
382	402	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1233 / 1233

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

411 / 411

position of stopcodon in wt / mu cDNA

1284 / 1284

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

52 / 52

chromosome

strand

-1

last intron/exon boundary

1153

theoretical NMD boundary in CDS

1051

length of CDS

1233

coding sequence (CDS) position

649

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

700

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

8053

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

101483814

original gDNA sequence snippet

CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT

altered gDNA sequence snippet

CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT

original cDNA sequence snippet

CAGACTCCCATGACATCCCTCGGGTCAGTCAGTACCGCCTT

altered cDNA sequence snippet

CAGACTCCCATGACATCCCTTGGGTCAGTCAGTACCGCCTT

wildtype AA sequence

mutated AA sequence

MQRLLFPPLR ALKGRQYLPL LAPRAAPRAQ CDCIRRPLRP GQYSTISEVA LQSGRGTVSL
PSKAAERVVG RWLLVCSGTV AGAVILGGVT RLTESGLSMV DWHLIKEMKP PTSQEEWEAE
FQRYQQFPEF KILNHDMTLT EFKFIWYMEY SHRMWGRLVG LVYILPAAYF WRKGWLSRGM
KGRVLALCGL VCFQGLLGWY MVKSGLEEKS DSHDIPWVSQ YRLAAHLGSA LVLYCASLWT
SLSLLLPPHK LPETHQLLQL RRFAHGTAGL VFLTALSGAF VAGLDAGLVY NSFPKMGESW
IPEDLFTFSP ILRNVFENPT MVQFDHRILG ITSVTAITVL YFLSRRIPLP RRTKMAAVTL
LALAYTQVGL GISTLLMYVP TPLAATHQSG SLALLTGALW LMNELRRVPK *

speed

0.95 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems