NM_005518.3(HMGCS2):c.858C>T (p.Ser286=) AND mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Sep 18, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000315225.3

Allele description [Variation Report for NM_005518.3(HMGCS2):c.858C>T (p.Ser286=)]

NM_005518.3(HMGCS2):c.858C>T (p.Ser286=)

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.858C>T (p.Ser286=)
HGVS:
  • NC_000001.11:g.119757431G>A
  • NG_013348.1:g.16502C>T
  • NM_001166107.1:c.732C>T
  • NM_005518.3:c.858C>T
  • NP_001159579.1:p.Ser244=
  • NP_005509.1:p.Ser286=
  • LRG_447t1:c.858C>T
  • LRG_447t2:c.732C>T
  • LRG_447:g.16502C>T
  • LRG_447p1:p.Ser286=
  • LRG_447p2:p.Ser244=
  • NC_000001.10:g.120300054G>A
Links:
dbSNP: rs1992376
NCBI 1000 Genomes Browser:
rs1992376
Molecular consequence:
  • NM_005518.3:c.858C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency (HMGCS2D)
Synonyms:
HMGCS2 DEFICIENCY; MITOCHONDRIAL HMG-CoA SYNTHASE DEFICIENCY
Identifiers:
MedGen: C2751532; Orphanet: 35701; OMIM: 605911

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000347908Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Jun 14, 2016)
germlineclinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV000648569Invitaecriteria provided, single submitter
Benign
(Sep 18, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Illumina Clinical Services Laboratory,Illumina, SCV000347908.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000648569.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 30, 2019

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