View genomic variant #0000020811

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.

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

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	0000020811	./.	-	-	c.2T>C	p.?	-	-	-	-
SDHA	00001116	XM_005248329.1	0000020811	./.	-	-	c.2T>C	p.?	-	-	-	-
SDHA	00001119	XM_005248330.1	0000020811	./.	-	-	c.2T>C	p.?	-	-	-	-
SDHA	00001115	XM_005248331.1	0000020811	./.	-	-	c.2T>C	p.?	-	-	-	-
SDHA	00001117	XR_241710.1	0000020811	./.	-	-	n.135T>C	-	-	-	-	-

10 per page 25 per page 50 per page 100 per page 250 per page 500 per page 1000 per page

Legend

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000462474; RCV000662887; RCV001017951;
Chromosome	5:218472..218472
ClinVar Allele ID	394857
Disease database name and identifier	MONDO:MONDO:0013602, MedGen:C3279992, OMIM:614165, Orphanet:29072|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MONDO:MONDO:0100294, MedGen:C5700310, OMIM:252011, Orphanet:3208
ClinVar preferred disease name	Paragangliomas 5|Hereditary cancer-predisposing syndrome|Mitochondrial complex II deficiency, nuclear type 1
HGVS variant names	NC 000005.9:g.218472T>C
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:CA16611812
Gene symbol:Gene id.	SDHA:6389
Molecular consequence	SO:0001582|initiator codon variant, SO:0001583|missense variant
Allele origin	germline
dbSNP ID	750380279
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000478025; RCV000649438; RCV001257552; RCV002438178; RCV002506172;
Chromosome	5:218472..218472
ClinVar Allele ID	406737
Disease database name and identifier	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:0013339, MedGen:C3150898, OMIM:613642, Orphanet:154|MONDO:MONDO:0031006, MedGen:C5543254, OMIM:619259|Human Phenotype Ontology:HP:0002859, MONDO:MONDO:0005212, MeSH:D012208, MedGen:C0035412, Orphanet:780
ClinVar preferred disease name	Mitochondrial complex II deficiency, nuclear type 1|Paragangliomas 5|Hereditary cancer-predisposing syndrome|not provided|Dilated cardiomyopathy 1GG|Neurodegeneration with ataxia and late-onset optic atrophy|Rhabdomyosarcoma
HGVS variant names	NC 000005.9:g.218472T>G
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:CA16618195
Gene symbol:Gene id.	SDHA:6389
Molecular consequence	SO:0001582|initiator codon variant, SO:0001583|missense variant
Allele origin	germline
dbSNP ID	750380279
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