View genomic variant #0000021158

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.

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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	0000021158	./.	-	-	c.1526C>T	p.(Ser509Leu)	-	-	-	-
SDHA	00001116	XM_005248329.1	0000021158	./.	-	-	c.1526C>T	p.(Ser509Leu)	-	-	-	-
SDHA	00001119	XM_005248330.1	0000021158	./.	-	-	c.1382C>T	p.(Ser461Leu)	-	-	-	-
SDHA	00001115	XM_005248331.1	0000021158	./.	-	-	c.1526C>T	p.(Ser509Leu)	-	-	-	-
SDHA	00001117	XR_241710.1	0000021158	./.	-	-	n.1463C>T	-	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000032786; RCV000695865;
Chromosome	5:240566..240566
ClinVar Allele ID	48185
Disease database name and identifier	MONDO:MONDO:0013602, MedGen:C3279992, OMIM:614165, Orphanet:29072|MONDO:MONDO:0100294, MedGen:C5700310, OMIM:252011, Orphanet:3208
ClinVar preferred disease name	Paragangliomas 5|Mitochondrial complex II deficiency, nuclear type 1
HGVS variant names	NC 000005.9:g.240566C>T
ClinVar review status	criteria provided, single submitter
Clinical Significance	Uncertain significance
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA130383|OMIM:600857.0007
Gene symbol:Gene id.	SDHA:6389
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	397514541
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000483714; RCV000575106; RCV000800769; RCV003401517; RCV003476157;
Chromosome	5:240566..240567
ClinVar Allele ID	406740
Disease database name and identifier	MONDO:MONDO:0013339, MedGen:C3150898, OMIM:613642, Orphanet:154|.|MONDO:MONDO:0015356, MeSH:D009386, MedGen:C0027672, Orphanet:140162|MedGen:C3661900|MONDO:MONDO:0100294, MedGen:C5700310, OMIM:252011, Orphanet:3208|MONDO:MONDO:0013602, MedGen:C3279992, OMIM:614165, Orphanet:29072
ClinVar preferred disease name	Dilated cardiomyopathy 1GG|SDHA-related condition|Hereditary cancer-predisposing syndrome|not provided|Mitochondrial complex II deficiency, nuclear type 1|Paragangliomas 5
HGVS variant names	NC 000005.9:g.240566 240567delinsGA
ClinVar review status	criteria provided, multiple submitters, no conflicts
Clinical Significance	Pathogenic/Likely pathogenic
Variant type	Indel
Sequence Ontology for variant type	SO:1000032
Variant clinical sources reported	ClinGen:CA16618198
Gene symbol:Gene id.	SDHA:6389
Molecular consequence	SO:0001587|nonsense
Allele origin	germline
dbSNP ID	1064793567
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