MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000261643
Querying Taster for transcript #2: ENST00000536205
Querying Taster for transcript #3: ENST00000537334
MT speed 0 s - this script 2.546925 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
COX10	disease_causing_automatic	0.999994429469004	simple_aae		affected	0	N204K	single base exchange	rs104894560		show file
COX10	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs104894560		show file
COX10	disease_causing_automatic	1	without_aae		affected	0		single base exchange	rs104894560		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999994429469004 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM001107)
known disease mutation: rs7522 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:14005547C>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.612C>A
cDNA.689C>A
g.32735C>A

AA changes

N204K Score: 94 explain score(s)

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

204

frameshift

known variant

Reference ID: rs104894560
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs7522 (pathogenic for Mitochondrial complex 4 deficiency, nuclear type 3) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001107)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001107)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001107)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.349	1
	1.877	1
(flanking)	1.796	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	32734	wt: 0.23 / mu: 0.49	wt: CCTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTT mu: CCTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTT	ccaa\|CTCC
Donor marginally increased	32729	wt: 0.9799 / mu: 0.9921 (marginal change - not scored)	wt: TGTGCTGCCAACTCC mu: TGTGCTGCCAAATCC	TGCT\|gcca
Donor increased	32738	wt: 0.36 / mu: 0.48	wt: AACTCCATCAATCAG mu: AAATCCATCAATCAG	CTCC\|atca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

204

mutated

not conserved

204

Ptroglodytes

all identical

ENSPTRG00000008790

204

Mmulatta

all identical

ENSMMUG00000016157

204

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000042148

203

Ggallus

all identical

ENSGALG00000001375

196

Trubripes

no homologue

Drerio

all identical

ENSDARG00000034309

201

Dmelanogaster

all identical

FBgn0032222

119

Celegans

all identical

Y46G5A.2

139

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
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

612

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

689

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

32735

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

14005547

original gDNA sequence snippet

CTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTTT

altered gDNA sequence snippet

CTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTTT

original cDNA sequence snippet

CTTGCATCCTGTGCTGCCAACTCCATCAATCAGTTTTTTGA

altered cDNA sequence snippet

CTTGCATCCTGTGCTGCCAAATCCATCAATCAGTTTTTTGA

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 YDLPGILARL SKIKLTALVV STTAAGFALA
PGPFDWPCFL LTSVGTGLAS CAAKSINQFF 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

0.14 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM001107)
known disease mutation: rs7522 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:14005547C>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

intron

DNA changes

g.32735C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.349	1
	1.877	1
(flanking)	1.796	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	32734	wt: 0.23 / mu: 0.49	wt: CCTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTT mu: CCTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTT	ccaa\|CTCC
Donor marginally increased	32729	wt: 0.9799 / mu: 0.9921 (marginal change - not scored)	wt: TGTGCTGCCAACTCC mu: TGTGCTGCCAAATCC	TGCT\|gcca
Donor increased	32738	wt: 0.36 / mu: 0.48	wt: AACTCCATCAATCAG mu: AAATCCATCAATCAG	CTCC\|atca

distance from splice site

25174

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

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

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

454 / 454

chromosome

strand

last intron/exon boundary

806

theoretical NMD boundary in CDS

302

length of CDS

756

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)

32735

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

14005547

original gDNA sequence snippet

CTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTTT

altered gDNA sequence snippet

CTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTTT

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

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

N/A

speed

0.10 s

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

known disease mutation at this position (HGMD CM001107)
known disease mutation: rs7522 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:14005547C>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

5'UTR

DNA changes

cDNA.292C>A
g.32735C>A

AA changes

N/A

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

N/A

frameshift

N/A

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.349	1
	1.877	1
(flanking)	1.796	1

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

splice sites

splice site change before start ATG (at aa -13) | splice site change before start ATG (at aa -12) |

effect	gDNA position	score	detection sequence	exon-intron border
Acc increased	32734	wt: 0.23 / mu: 0.49	wt: CCTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTT mu: CCTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTT	ccaa\|CTCC
Donor marginally increased	32729	wt: 0.9799 / mu: 0.9921 (marginal change - not scored)	wt: TGTGCTGCCAACTCC mu: TGTGCTGCCAAATCC	TGCT\|gcca
Donor increased	32738	wt: 0.36 / mu: 0.48	wt: AACTCCATCAATCAG mu: AAATCCATCAATCAG	CTCC\|atca

distance from splice site

Kozak consensus sequence altered?

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)

292

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

32735

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

14005547

original gDNA sequence snippet

CTTGCATCCTGTGCTGCCAACTCCATCAATCAGGTCAGTTT

altered gDNA sequence snippet

CTTGCATCCTGTGCTGCCAAATCCATCAATCAGGTCAGTTT

original cDNA sequence snippet

CTTGCATCCTGTGCTGCCAACTCCATCAATCAGTTTTTTGA

altered cDNA sequence snippet

CTTGCATCCTGTGCTGCCAAATCCATCAATCAGTTTTTTGA

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

0.20 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

Problems