View genomic variant #0000015543

Variant on transcripts

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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

2 entries on 1 page. Showing entries 1 - 2.

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Gene	Transcript ID	Transcript	Variant ID	Affects function	Location	Exon	DNA change (cDNA)	Protein	PolyPhen	GVS function	Splice distance	SIFT
HMGCS2	00000819	NM_001166107.1	0000015543	./.	-	-	c.73C>G	p.(Pro25Ala)	-	-	-	-
HMGCS2	00000820	NM_005518.3	0000015543	./.	-	-	c.73C>G	p.(Pro25Ala)	-	-	-	-

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ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV000185971; RCV000647361;
Chromosome	1:120311395..120311395
Allele frequencies from ESP	0.00008
Allele frequencies from ExAC	0.00037
ClinVar Allele ID	199942
Disease database name and identifier	MedGen:CN169374|MONDO:MONDO:0011614, MedGen:C2751532, OMIM:605911, Orphanet:35701
ClinVar preferred disease name	not specified|3-hydroxy-3-methylglutaryl-CoA synthase deficiency
HGVS variant names	NC 000001.10:g.120311395G>C
ClinVar review status	criteria provided, conflicting interpretations
Clinical Significance	Conflicting interpretations of pathogenicity
Conflicting clinical significance	Uncertain significance(1)|Likely benign(1)
Variant type	single nucleotide variant
Sequence Ontology for variant type	SO:0001483
Variant clinical sources reported	ClinGen:CA312636
Gene symbol:Gene id.	HMGCS2:3158|LOC122094910:122094910
Molecular consequence	SO:0001583|missense variant
Allele origin	germline
dbSNP ID	144744634
Variant Flags	:

ClinVar @ MSeqDR as full content XML tree

ClinVar @ MSeqDR
RCVaccession	RCV001449675;
Chromosome	1:120311395..120311396
ClinVar Allele ID	1108852
Disease database name and identifier	MONDO:MONDO:0011614, MedGen:C2751532, OMIM:605911, Orphanet:35701
ClinVar preferred disease name	3-hydroxy-3-methylglutaryl-CoA synthase deficiency
HGVS variant names	NC 000001.10:g.120311396dup
ClinVar review status	no assertion criteria provided
Clinical Significance	Pathogenic
Variant type	Duplication
Sequence Ontology for variant type	SO:1000035
Gene symbol:Gene id.	HMGCS2:3158|LOC122094910:122094910
Molecular consequence	SO:0001589|frameshift variant
Allele origin	maternal
dbSNP ID	2101283564
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