View genomic variant #0000002616

Chromosome	17
Allele	Unknown
Affects function (as reported)	Affects function
Affects function (by curator)	Affects function
Type	subst
DNA change (genomic) (Relative to hg19 / GRCh37)	g.14110205A>G
Published as	-
GERP	4.960
Segregation	-
DB-ID	COX10_000004 See all 2 reported entries
MSCV	MSCV_0002616
dbSNP ID	rs104894557
Frequency	-
Sources	; clinvar; ensembl;
Reference	12928484
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	Variant not found in online data sets
Owner	LOVD

Variant on transcripts

Legend

Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column's header and hold it still. Below, a more detailed description is shown per column.

Affects function: The variant's effect on the protein's function, in the format 'R/C' where R is the value reported by the source and C is the value concluded by the curator; '+' indicating the variant affects function, '+?' probably affects function, '+*' affects function, not associated with individual's disease phenotype, '#' affects function, not associated with any known disease phenotype, '-' does not affect function, '-?' probably does not affect function, '?' effect unknown, '.' effect not classified.

Location: Location of variant at DNA level; note that the variant location can also be derived from the variant description.
All options:

5' gene flanking
5' UTR
Exon
Intron
3' UTR
3' gene flanking

Exon: Number of exon/intron containing variant; 2 = exon 2, 12i = intron 12, 2i_7i = exons 3 to 7, 8i_9 = border intron 8/exon 9.

DNA change (cDNA): Description of variant at DNA level, based on a coding DNA reference sequence (following HGVS recommendations); e.g. c.123C>T, c.123_145del, c.123_126dup.

Protein: Description of variant at protein level (following HGVS recommendations).

p.(Arg345Pro) = change predicted from DNA (RNA not analysed)
p.Arg345Pro = change derived from RNA analysis
p.? = unknown effect
p.0? = probably no protein produced

PolyPhen: Effect of variant, predicted by PolyPhen.
All options:

benign = Benign
possiblyDamaging = Possibly damaging
probablyDamaging = Probably damaging
noPrediction = No prediction

GVS function: The functional annotation of this position from the Genome Variation Server.
All options:

intergenic
near-gene-5
utr-5
coding
coding-near-splice
coding-synonymous
coding-synonymous-near-splice
codingComplex
codingComplex-near-splice
frameshift
frameshift-near-splice
missense
missense-near-splice
splice-5
intron
splice-3
stop-gained
stop-gained-near-splice
stop-lost
stop-lost-near-splice
utr-3
near-gene-3

Splice distance: The distance to the nearest splice site.

SIFT: SIFT Annotation

1 entry on 1 page. Showing entry 1.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
COX10	00000076	NM_001303.3	0000002616	+/+	-	7/7	c.1007A>G	p.(Asp336Gly)	probably_damaging(1)	missense_variant	-	deleterious(0)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000007961;
Chromosome	17:14110205..14110205
ClinVar Allele ID	22565
Disease database name and identifier	MONDO:MONDO:0033635, MedGen:C5436682, OMIM:619046
ClinVar preferred disease name	Mitochondrial complex 4 deficiency, nuclear type 3
HGVS variant names	NC 000017.10:g.14110205A>G
ClinVar review status	no assertion criteria provided
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA118863\|OMIM:602125.0005\|UniProtKB:Q12887#VAR 026565
Gene symbol:Gene id.	COX10:1352
Molecular consequence	SO:0001583\|missense variant
Allele origin	germline
dbSNP ID	104894557
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000007960; RCV000995747;
Chromosome 17:14110205..14110205
Allele frequencies from ExAC 0.00006
Allele frequencies from TGP 0.00020
ClinVar Allele ID 22564
Disease database name and identifier MONDO:MONDO:0033635, MedGen:C5436682, OMIM:619046|MONDO:MONDO:0009068, MedGen:C5435656, OMIM:220110, Orphanet:254905
ClinVar preferred disease name Mitochondrial complex 4 deficiency, nuclear type 3|Cytochrome-c oxidase deficiency disease
HGVS variant names NC 000017.10:g.14110205A>T
ClinVar review status criteria provided, multiple submitters, no conflicts
Clinical Significance Pathogenic/Likely pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA118862|OMIM:602125.0004|UniProtKB:Q12887#VAR 026566
Gene symbol:Gene id. COX10:1352
Molecular consequence SO:0001583|missense variant
Allele origin
dbSNP ID 104894557
Variant Flags
:

ClinVar @ MSeqDR as full content XML tree

MSeqDR View Variant at Gbrowse

Mitomap Mitochondrial Variant Phenotype Information:

None

Ensembl Variant Phenotype Information:

None