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: ENST00000429152
Querying Taster for transcript #2: ENST00000261643
Querying Taster for transcript #3: ENST00000536205
Querying Taster for transcript #4: ENST00000537334
MT speed 0 s - this script 4.255385 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COX10	polymorphism_automatic	0.00703727181845704	simple_aae		affected		D9N	single base exchange	rs2072279		show file
COX10	polymorphism_automatic	0.995479556275232	simple_aae		affected		R159Q	single base exchange	rs2072279		show file
COX10	polymorphism_automatic	0.9994848917723	simple_aae		affected		R159Q	single base exchange	rs2072279		show file
COX10	polymorphism_automatic	1	without_aae		affected			single base exchange	rs2072279		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.992962728181543 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:13980350G>AN/A show variant in all transcripts IGV

HGNC symbol

COX10

Ensembl transcript ID

ENST00000536205

Genbank transcript ID

N/A

UniProt peptide

Q12887

alteration type

single base exchange

alteration region

CDS

DNA changes

c.25G>A
cDNA.478G>A
g.7538G>A

AA changes

D9N Score: 23 explain score(s)

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

frameshift

known variant

Reference ID: rs2072279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	568	1187	1755
ExAC	14893	2981	17874

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.418	0.891
	3.914	0.89
(flanking)	-2.099	0.128

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	7534	0.71	mu: TTTTGGCTCAACTAT	TTGG\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

no alignment

ENSPTRG00000008790

n/a

Mmulatta

no alignment

ENSMMUG00000016157

n/a

Fcatus

no homologue

Mmusculus

no alignment

ENSMUSG00000042148

n/a

Ggallus

no alignment

ENSGALG00000001375

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000034309

n/a

Dmelanogaster

no alignment

FBgn0032222

n/a

Celegans

no alignment

Y46G5A.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
174	194	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
257	277	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	300	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
303	303	CONFLICT	A -> T (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
309	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
364	384	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	Y -> H (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
411	431	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

756 / 756

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

252 / 252

position of stopcodon in wt / mu cDNA

1209 / 1209

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

454 / 454

chromosome

strand

last intron/exon boundary

806

theoretical NMD boundary in CDS

302

length of CDS

756

coding sequence (CDS) position

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

478

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

7538

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

13980350

original gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

original cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

wildtype AA sequence

MICQEFWLDY PKSNSQFFEV PFDSNMNRTK NRPLVRGQIS PLLAVSFATC CAVPGVAILT
LGVNPLTGAL GLFNIFLYTC CYTPLKRISI ANTWVGAVVG AIPPVMGWTA ATGSLDAGAF
LLGGILYSWQ FPHFNALSWG LREDYSRGGY CMMSVTHPGL CRRVALRHCL ALLVLSAAAP
VLDITTWTFP IMALPINAYI SYLGFRFYVD ADRRSSRRLF FCSLWHLPLL LLLMLTCKRP
SGGGDAGPPP S*

mutated AA sequence

MICQEFWLNY PKSNSQFFEV PFDSNMNRTK NRPLVRGQIS PLLAVSFATC CAVPGVAILT
LGVNPLTGAL GLFNIFLYTC CYTPLKRISI ANTWVGAVVG AIPPVMGWTA ATGSLDAGAF
LLGGILYSWQ FPHFNALSWG LREDYSRGGY CMMSVTHPGL CRRVALRHCL ALLVLSAAAP
VLDITTWTFP IMALPINAYI SYLGFRFYVD ADRRSSRRLF FCSLWHLPLL LLLMLTCKRP
SGGGDAGPPP S*

speed

0.88 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: 0.0045204437247678 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:13980350G>AN/A show variant in all transcripts IGV

HGNC symbol

COX10

Ensembl transcript ID

ENST00000429152

Genbank transcript ID

N/A

UniProt peptide

Q12887

alteration type

single base exchange

alteration region

CDS

DNA changes

c.476G>A
cDNA.586G>A
g.7538G>A

AA changes

R159Q Score: 43 explain score(s)

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

159

frameshift

known variant

Reference ID: rs2072279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	568	1187	1755
ExAC	14893	2981	17874

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.418	0.891
	3.914	0.89
(flanking)	-2.099	0.128

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	7534	0.71	mu: TTTTGGCTCAACTAT	TTGG\|ctca

distance from splice site

290

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

159

mutated

all conserved

159

Ptroglodytes

all identical

ENSPTRG00000008790

159

Mmulatta

all identical

ENSMMUG00000016157

159

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000042148

158

Ggallus

all identical

ENSGALG00000001375

151

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034309

165

Dmelanogaster

no alignment

FBgn0032222

n/a

Celegans

no alignment

Y46G5A.2

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
174	194	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
257	277	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	300	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
303	303	CONFLICT	A -> T (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
309	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
364	384	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	Y -> H (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
411	431	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

516 / 516

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

172 / 172

position of stopcodon in wt / mu cDNA

626 / 626

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

111 / 111

chromosome

strand

last intron/exon boundary

288

theoretical NMD boundary in CDS

127

length of CDS

516

coding sequence (CDS) position

476

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

586

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

7538

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

13980350

original gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

original cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

wildtype AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILARL SKIKLTGTLF F*

mutated AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILAQL SKIKLTGTLF F*

speed

0.88 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.000515108227700298 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:13980350G>AN/A show variant in all transcripts IGV

HGNC symbol

COX10

Ensembl transcript ID

ENST00000261643

Genbank transcript ID

NM_001303

UniProt peptide

Q12887

alteration type

single base exchange

alteration region

CDS

DNA changes

c.476G>A
cDNA.553G>A
g.7538G>A

AA changes

R159Q Score: 43 explain score(s)

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

159

frameshift

known variant

Reference ID: rs2072279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	568	1187	1755
ExAC	14893	2981	17874

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.418	0.891
	3.914	0.89
(flanking)	-2.099	0.128

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	7534	0.71	mu: TTTTGGCTCAACTAT	TTGG\|ctca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

159

mutated

all conserved

159

Ptroglodytes

all identical

ENSPTRG00000008790

159

Mmulatta

all identical

ENSMMUG00000016157

159

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000042148

158

Ggallus

all identical

ENSGALG00000001375

151

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034309

165

Dmelanogaster

all conserved

FBgn0032222

LSQYK

Celegans

not conserved

Y46G5A.2

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
174	194	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
257	277	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	300	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
303	303	CONFLICT	A -> T (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
309	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
364	384	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	Y -> H (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
411	431	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

1332 / 1332

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

444 / 444

position of stopcodon in wt / mu cDNA

1409 / 1409

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

78 / 78

chromosome

strand

last intron/exon boundary

1006

theoretical NMD boundary in CDS

878

length of CDS

1332

coding sequence (CDS) position

476

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

553

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

7538

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

13980350

original gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

original cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered cDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

wildtype AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILARL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRPLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*

mutated AA sequence

MAASPHTLSS RLLTGCVGGS VWYLERRTIQ DSPHKFLHLL RNVNKQWITF QHFSFLKRMY
VTQLNRSHNQ QVRPKPEPVA SPFLEKTSSG QAKAEIYEMR PLSPPSLSLS RKPNEKELIE
LEPDSVIEDS IDVGKETKEE KRWKEMKLQV YDLPGILAQL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAANSINQFF EVPFDSNMNR TKNRPLVRGQ ISPLLAVSFA
TCCAVPGVAI LTLGVNPLTG ALGLFNIFLY TCCYTPLKRI SIANTWVGAV VGAIPPVMGW
TAATGSLDAG AFLLGGILYS WQFPHFNALS WGLREDYSRG GYCMMSVTHP GLCRRVALRH
CLALLVLSAA APVLDITTWT FPIMALPINA YISYLGFRFY VDADRRSSRR LFFCSLWHLP
LLLLLMLTCK RPSGGGDAGP PPS*

speed

0.44 s

mutation t@sting

documentation

Prediction

polymorphism

Model: without_aae, prob: 1.44894381767654e-30 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:13980350G>AN/A show variant in all transcripts IGV

HGNC symbol

COX10

Ensembl transcript ID

ENST00000537334

Genbank transcript ID

N/A

UniProt peptide

Q12887

alteration type

single base exchange

alteration region

intron

DNA changes

g.7538G>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs2072279

database	homozygous (A/A)	heterozygous	allele carriers
1000G	568	1187	1755
ExAC	14893	2981	17874

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.418	0.891
	3.914	0.89
(flanking)	-2.099	0.128

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

splice site change before start ATG (at aa -50) |

effect	gDNA position	score	detection sequence	exon-intron border
Donor gained	7534	0.71	mu: TTTTGGCTCAACTAT	TTGG\|ctca

distance from splice site

2577

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
1	1	TRANSIT	Mitochondrion (Potential). - EXACT POSITION UNKNOWN	might get lost (downstream of altered splice site)
174	194	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
235	255	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
257	277	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
280	300	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
303	303	CONFLICT	A -> T (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
309	329	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
364	384	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
394	394	CONFLICT	Y -> H (in Ref. 1; AAA21148).	might get lost (downstream of altered splice site)
411	431	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

332 / 332

chromosome

strand

last intron/exon boundary

609

theoretical NMD boundary in CDS

227

length of CDS

681

coding sequence (CDS) position

N/A

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

N/A

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

7538

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

13980350

original gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCGACTATCCAAAATCAAACTCA

altered gDNA sequence snippet

TTTGCCAGGAATTTTGGCTCAACTATCCAAAATCAAACTCA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MNRTKNRPLV RGQISPLLAV SFATCCAVPG VAILTLGVNP LTGALGLFNI FLYTCCYTPL
KRISIANTWV GAVVGAIPPV MGWTAATGSL DAGAFLLGGI LYSWQFPHFN ALSWGLREDY
SRGGYCMMSV THPGLCRRVA LRHCLALLVL SAAAPVLDIT TWTFPIMALP INAYISYLGF
RFYVDADRRS SRRLFFCSLW HLPLLLLLML TCKRPSGGGD AGPPPS*

mutated AA sequence

N/A

speed

0.46 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems