View genomic variant #0000026020

Variant on transcripts

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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

3 entries on 1 page. Showing entries 1 - 3.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
ACO2	00000021	NM_001098.2	0000026020	./.	-	-	c.719G>C	p.(Gly240Ala)	-	-	-	-
ACO2	00000020	XM_005261621.1	0000026020	./.	-	-	c.470G>C	p.(Gly157Ala)	-	-	-	-
ACO2	00000019	XM_005261622.1	0000026020	./.	-	-	c.129-2735G>C	p.(=)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000196947; RCV000764400; RCV001073882; RCV001197153; RCV001333751;
Chromosome	22:41911805..41911805
Allele frequencies from ESP	0.00108
Allele frequencies from TGP	0.00020
ClinVar Allele ID	211934
Disease database name and identifier	Human Phenotype Ontology:HP:0000556, Human Phenotype Ontology:HP:0007736, Human Phenotype Ontology:HP:0007910, Human Phenotype Ontology:HP:0007974, Human Phenotype Ontology:HP:0007982, MONDO:MONDO:0019118, MeSH:D058499, MedGen:C0854723, Orphanet:71862|MONDO:MONDO:0013802, MedGen:C3281192, OMIM:614559, Orphanet:313850|MONDO:MONDO:0014571, MedGen:C4225384, OMIM:616289|MedGen:C3661900
ClinVar preferred disease name	Retinal dystrophy|Infantile cerebellar-retinal degeneration|Optic atrophy 9|not provided
HGVS variant names	NC 000022.10:g.41911805G>C
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA321374
Gene symbol:Gene id.	ACO2:50
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	141878785
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