NM_005518.3(HMGCS2):c.685+2T>A AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 23, 2013
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000185974.2

Allele description

NM_005518.3(HMGCS2):c.685+2T>A

Gene:

HMGCS2:3-hydroxy-3-methylglutaryl-CoA synthase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p12

Genomic location:

Preferred name:

NM_005518.3(HMGCS2):c.685+2T>A

HGVS:

NC_000001.11:g.119759862A>T
NG_013348.1:g.14071T>A
NM_001166107.1:c.560-580T>A
NM_005518.3:c.685+2T>A
LRG_447t1:c.685+2T>A
LRG_447t2:c.560-580T>A
LRG_447:g.14071T>A
NC_000001.10:g.120302485A>T

Links:

dbSNP: rs796051979

NCBI 1000 Genomes Browser:

rs796051979

Molecular consequence:

NM_001166107.1:c.560-580T>A - intron variant - [Sequence Ontology: SO:0001627]
NM_005518.3:c.685+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000238932	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Sep 23, 2013)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000238932

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Sep 23, 2013)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000238932.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

c.685+2 T>A: IVS3+2 T>A in intron 3 of the HMGCS2 gene (NM_005518.3). The c.685+2 T>A splice site mutation destroys the canonical splice donor site in intron 3. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. Although this mutation has not been previously reported to our knowledge, it is expected to be a pathogenic mutation. The variant is found in FAO-MET panel(s).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 11, 2017

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