View genomic variant #0000020813

Chromosome	5
Allele	Unknown
Affects function (as reported)	Effect unknown
Affects function (by curator)	Effect unknown
Type	-
DNA change (genomic) (Relative to hg19 / GRCh37)	g.218475C>T
Published as	-
GERP	-
Segregation	-
DB-ID	SDHA_000377
MSCV	MSCV_0020813
dbSNP ID	-
Frequency	-
Sources	; clinvar;
Reference	-
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

5 entries on 1 page. Showing entries 1 - 5.

Legend

Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
SDHA	00001118	NM_004168.2	0000020813	./.	-	-	c.5C>T	p.(Ser2Leu)	-	-	-	-
SDHA	00001116	XM_005248329.1	0000020813	./.	-	-	c.5C>T	p.(Ser2Leu)	-	-	-	-
SDHA	00001119	XM_005248330.1	0000020813	./.	-	-	c.5C>T	p.(Ser2Leu)	-	-	-	-
SDHA	00001115	XM_005248331.1	0000020813	./.	-	-	c.5C>T	p.(Ser2Leu)	-	-	-	-
SDHA	00001117	XR_241710.1	0000020813	./.	-	-	n.138C>T	-	-	-	-	-

Legend

ClinVar @ MSeqDR
RCVaccession	RCV000797937;
Chromosome	5:218475..218475
ClinVar Allele ID	633848
Disease database name and identifier	MONDO:MONDO:0100294, MedGen:C5700310, OMIM:252011, Orphanet:3208\|MONDO:MONDO:0013602, MedGen:C3279992, OMIM:614165, Orphanet:29072
ClinVar preferred disease name	Mitochondrial complex II deficiency, nuclear type 1\|Paragangliomas 5
HGVS variant names	NC 000005.9:g.218475C>A
ClinVar review status	criteria provided, single submitter
Clinical Significance	Pathogenic
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Gene symbol:Gene id.	SDHA:6389
Molecular consequence	SO:0001587\|nonsense
Allele origin	germline
dbSNP ID	780064103
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession RCV000473246; RCV000569083; RCV001153199; RCV001153200; RCV001153198; RCV003225073;
Chromosome 5:218475..218475
Allele frequencies from ExAC 0.00003
ClinVar Allele ID 395462
Disease database name and identifier MONDO:MONDO:0009723, MedGen:C0023264, OMIM:256000, Orphanet:506|MONDO:MONDO:0100294, MedGen:C5700310, OMIM:252011, Orphanet:3208|MONDO:MONDO:0013602, MedGen:C3279992, OMIM:614165, Orphanet:29072|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MedGen:C3661900|MONDO:MONDO:0017366, MedGen:C1708353, Orphanet:29072
ClinVar preferred disease name Leigh syndrome|Mitochondrial complex II deficiency, nuclear type 1|Paragangliomas 5|Hereditary cancer-predisposing syndrome|not provided|Hereditary pheochromocytoma-paraganglioma
HGVS variant names NC 000005.9:g.218475C>T
ClinVar review status criteria provided, conflicting interpretations
Clinical Significance Conflicting interpretations of pathogenicity
Conflicting clinical significance Uncertain significance(6)|Likely benign(1)
Variant type single nucleotide variant
Sequence Ontology for variant type SO:0001483
Variant clinical sources reported ClinGen:CA3172677
Gene symbol:Gene id. SDHA:6389
Molecular consequence SO:0001583|missense variant
Allele origin germline
dbSNP ID 780064103
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