View genomic variant #0000000715

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.14063243C>T
Published as	-
GERP	4.970
Segregation	-
DB-ID	COX10_000003 See all 2 reported entries
MSCV	MSCV_0000715
dbSNP ID	rs104894556
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	0000000715	+/+	-	5/7	c.674C>T	p.(Pro225Leu)	probably_damaging(0.998)	missense_variant	-	tolerated(0.68)

Legend

ClinVar @ MSeqDR
RCVaccession	RCV002861505;
Chromosome	17:14063243..14063243
ClinVar Allele ID	2074962
Disease database name and identifier	MedGen:CN517202
ClinVar preferred disease name	not provided
HGVS variant names	NC 000017.10:g.14063243C>G
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	COX10:1352
Molecular consequence	SO:0001583\|missense variant
Allele origin	germline
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000007959;
Chromosome 17:14063243..14063243
Allele frequencies from ExAC 0.00001
Allele frequencies from TGP 0.00020
ClinVar Allele ID 22563
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.14063243C>T
ClinVar review status criteria provided, single submitter
Clinical Significance Likely pathogenic
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA118861|OMIM:602125.0003|UniProtKB:Q12887#VAR 026564
Gene symbol:Gene id. COX10:1352
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 104894556
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