NM_000170.3(GLDC):c.2019T>A (p.Tyr673Ter) AND Non-ketotic hyperglycinemia

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 27, 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:: RCV001994499.3

Allele description

NM_000170.3(GLDC):c.2019T>A (p.Tyr673Ter)

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.2019T>A (p.Tyr673Ter)

HGVS:

NC_000009.12:g.6558592A>T
NG_016397.1:g.92101T>A
NM_000170.3:c.2019T>AMANE SELECT
NP_000161.2:p.Tyr673Ter
LRG_643:g.92101T>A
NC_000009.11:g.6558592A>T

Protein change:

Y673*

Links:

dbSNP: rs774506115

NCBI 1000 Genomes Browser:

rs774506115

Molecular consequence:

NM_000170.3:c.2019T>A - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002229792	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 27, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26179960, 16601880, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002229792

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 27, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia.

Swanson MA, Coughlin CR Jr, Scharer GH, Szerlong HJ, Bjoraker KJ, Spector EB, Creadon-Swindell G, Mahieu V, Matthijs G, Hennermann JB, Applegarth DA, Toone JR, Tong S, Williams K, Van Hove JL.

Ann Neurol. 2015 Oct;78(4):606-18. doi: 10.1002/ana.24485. Epub 2015 Aug 10. Erratum in: Ann Neurol. 2016 Mar;79(3):505. doi: 10.1002/ana.24600.

PubMed [citation]

PMID:: 26179960
PMCID:: PMC4767401

Genetic heterogeneity of the GLDC gene in 28 unrelated patients with glycine encephalopathy.

Conter C, Rolland MO, Cheillan D, Bonnet V, Maire I, Froissart R.

J Inherit Metab Dis. 2006 Feb;29(1):135-42.

PubMed [citation]

PMID:: 16601880

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002229792.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with non-ketotic hyperglycinemia (PMID: 26179960). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr673*) in the GLDC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GLDC are known to be pathogenic (PMID: 16601880).

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

Last Updated: Jun 9, 2024

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