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NC_000009.12:g.(?_6532997)_(6645519_?)del AND Non-ketotic hyperglycinemia

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 14, 2018
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:
RCV000559085.3

Allele description [Variation Report for NC_000009.12:g.(?_6532997)_(6645519_?)del]

NC_000009.12:g.(?_6532997)_(6645519_?)del

Genes:
LOC130001537:ATAC-STARR-seq lymphoblastoid active region 28187 [Gene]
LOC130001538:ATAC-STARR-seq lymphoblastoid active region 28191 [Gene]
LOC126860573:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:6566198-6567397 [Gene]
LOC113839554:Sharpr-MPRA regulatory region 10661 [Gene]
GLDC:glycine decarboxylase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9p24.1
Genomic location:
Preferred name:
NC_000009.12:g.(?_6532997)_(6645519_?)del
HGVS:
  • NC_000009.12:g.(?_6532997)_(6645519_?)del
  • NC_000009.11:g.(?_6532997)_(6645519_?)del

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
SCV000636345Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 14, 2018) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Genomic deletion within GLDC is a major cause of non-ketotic hyperglycinaemia.

Kanno J, Hutchin T, Kamada F, Narisawa A, Aoki Y, Matsubara Y, Kure S.

J Med Genet. 2007 Mar;44(3):e69.

PubMed [citation]
PMID:
17361008
PMCID:
PMC2598024

Mutation analysis of glycine decarboxylase, aminomethyltransferase and glycine cleavage system protein-H genes in 13 unrelated families with glycine encephalopathy.

Azize NA, Ngah WZ, Othman Z, Md Desa N, Chin CB, Md Yunus Z, Mohan A, Hean TS, Syed Zakaria SZ, Lock-Hock N.

J Hum Genet. 2014 Nov;59(11):593-7. doi: 10.1038/jhg.2014.69. Epub 2014 Sep 18.

PubMed [citation]
PMID:
25231368
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000636345.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the GLDC gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. A similar whole gene deletion has been reported in the literature in individuals affected with glycine encephalopathy (PMID: 17361008, 26947380, 25231368, 28468868). Loss-of-function variants in GLDC are known to be pathogenic (PMID: 16601880). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Feb 20, 2024