View genomic variant #0000017309

Chromosome	13
Allele	Unknown
Affects function (as reported)	Probably affects function
Affects function (by curator)	Probably affects function
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.48571013G>A
Published as	-
GERP	-
Segregation	-
DB-ID	SUCLA2_000041
MSCV	MSCV_0017309
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
Variant remarks	-
Genetic origin	-
Variant_disease	-
Average frequency (large NGS studies)	0.00023 View details
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

4 entries on 1 page. Showing entries 1 - 4.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
SUCLA2	00000313	NM_003850.2	0000017309	./.	-	-	c.236C>T	p.(Ser79Leu)	-	-	-	-
SUCLA2	00000312	XM_005266579.1	0000017309	./.	-	-	c.62C>T	-	-	-	-	-
SUCLA2	00000315	XM_005266580.1	0000017309	./.	-	-	c.62C>T	-	-	-	-	-
SUCLA2	00000314	XM_005266581.1	0000017309	./.	-	-	c.-264C>T	p.(=)	-	-	-	-

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ClinVar @ MSeqDR
RCVaccession	RCV000186185; RCV000449628; RCV001089257; RCV003278685;
Chromosome	13:48571013..48571013
Allele frequencies from ESP	0.00023
Allele frequencies from ExAC	0.00062
Allele frequencies from TGP	0.00020
ClinVar Allele ID	200273
Disease database name and identifier	MeSH:D030342, MedGen:C0950123\|Human Phenotype Ontology:HP:0000754, Human Phenotype Ontology:HP:0001255, Human Phenotype Ontology:HP:0001263, Human Phenotype Ontology:HP:0001277, Human Phenotype Ontology:HP:0001292, Human Phenotype Ontology:HP:0002433, Human Phenotype Ontology:HP:0002473, Human Phenotype Ontology:HP:0002532, Human Phenotype Ontology:HP:0006793, Human Phenotype Ontology:HP:0006867, Human Phenotype Ontology:HP:0006885, Human Phenotype Ontology:HP:0006935, Human Phenotype Ontology:HP:0007005, Human Phenotype Ontology:HP:0007094, Human Phenotype Ontology:HP:0007106, Human Phenotype Ontology:HP:0007174, Human Phenotype Ontology:HP:0007224, Human Phenotype Ontology:HP:0007228, Human Phenotype Ontology:HP:0007342, Human Phenotype Ontology:HP:0025356, MedGen:C0557874\|MONDO:MONDO:0012791, MedGen:C2749864, OMIM:612073, Orphanet:1933\|MedGen:C3661900
ClinVar preferred disease name	Inborn genetic diseases\|Global developmental delay\|Mitochondrial DNA depletion syndrome, encephalomyopathic form with methylmalonic aciduria\|not provided
HGVS variant names	NC 000013.10:g.48571013G>A
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(3)\|Likely benign(2)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA313028
Gene symbol:Gene id.	SUCLA2:8803
Molecular consequence	SO:0001583\|missense variant
Allele origin	germline
dbSNP ID	142289138
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