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NM_000170.3(GLDC):c.2008G>C (p.Val670Leu) AND Non-ketotic hyperglycinemia

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 15, 2021
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:
RCV002040937.6

Allele description [Variation Report for NM_000170.3(GLDC):c.2008G>C (p.Val670Leu)]

NM_000170.3(GLDC):c.2008G>C (p.Val670Leu)

Gene:
GLDC:glycine decarboxylase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9p24.1
Genomic location:
Preferred name:
NM_000170.3(GLDC):c.2008G>C (p.Val670Leu)
HGVS:
  • NC_000009.12:g.6558603C>G
  • NG_016397.1:g.92090G>C
  • NM_000170.3:c.2008G>CMANE SELECT
  • NP_000161.2:p.Val670Leu
  • LRG_643:g.92090G>C
  • NC_000009.11:g.6558603C>G
Protein change:
V670L
Links:
dbSNP: rs767864486
NCBI 1000 Genomes Browser:
rs767864486
Molecular consequence:
  • NM_000170.3:c.2008G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Non-ketotic hyperglycinemia
Synonyms:
Glycine encephalopathy; Nonketotic hyperglycinemia
Identifiers:
MONDO: MONDO:0011612; MedGen: C0751748; Orphanet: 407; OMIM: PS605899; Human Phenotype Ontology: HP:0008288

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002314068Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 15, 2021) 		germlineclinical testing

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

Help

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. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002314068.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with GLDC-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces valine with leucine at codon 670 of the GLDC protein (p.Val670Leu). The valine residue is moderately conserved and there is a small physicochemical difference between valine and leucine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024