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NM_000170.3(GLDC):c.499G>T (p.Glu167Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Aug 10, 2021)
Last evaluated:
Oct 23, 2020
Accession:
VCV000370365.11
Variation ID:
370365
Description:
single nucleotide variant
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NM_000170.3(GLDC):c.499G>T (p.Glu167Ter)

Allele ID
357818
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.1
Genomic location
9: 6610328 (GRCh38) GRCh38 UCSC
9: 6610328 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_643:g.40365G>T
LRG_643t1:c.499G>T LRG_643p1:p.Glu167Ter
NC_000009.11:g.6610328C>A
... more HGVS
Protein change
E167*
Other names
-
Canonical SPDI
NC_000009.12:6610327:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00080 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
The Genome Aggregation Database (gnomAD) 0.00012
Trans-Omics for Precision Medicine (TOPMed) 0.00020
1000 Genomes Project 0.00080
Trans-Omics for Precision Medicine (TOPMed) 0.00004
Links
ClinGen: CA4981110
dbSNP: rs191905539
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 5 criteria provided, multiple submitters, no conflicts Oct 23, 2020 RCV000412474.9
Pathogenic 1 criteria provided, single submitter Jan 18, 2016 RCV000624546.1
Pathogenic 1 criteria provided, single submitter Mar 12, 2019 RCV001556638.2

Clinical features observed in individuals with this variant

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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GLDC - - GRCh38
GRCh37
1080 1273

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Jul 02, 2020)
criteria provided, single submitter
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000695761.2
Submitted: (Aug 06, 2020)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: GLDC c.499G>T (p.Glu167X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Jan 18, 2016)
criteria provided, single submitter
Method: clinical testing
Inborn genetic diseases
Allele origin: germline
Ambry Genetics
Accession: SCV000741325.2
Submitted: (Oct 09, 2020)
Evidence details
Pathogenic
(Oct 23, 2020)
criteria provided, single submitter
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: germline
Invitae
Accession: SCV000636407.4
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Glu167*) in the GLDC gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Mar 12, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001778253.1
Submitted: (Aug 10, 2021)
Evidence details
Comment:
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not … (more)
Likely pathogenic
(Oct 31, 2016)
no assertion criteria provided
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: unknown
Counsyl
Accession: SCV000485665.2
Submitted: (Aug 05, 2019)
Evidence details
Publications
PubMed (1)
Pathogenic
(Jun 29, 2016)
no assertion criteria provided
Method: research
Non-ketotic hyperglycinemia
Allele origin: germline
Division of Human Genetics,Children's Hospital of Philadelphia
Study: CSER-PediSeq
Accession: SCV000536876.1
Submitted: (Jan 23, 2017)
Evidence details
Pathogenic
(Sep 16, 2020)
no assertion criteria provided
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: germline
Natera, Inc.
Accession: SCV001458172.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
The genetic basis of classic nonketotic hyperglycinemia due to mutations in GLDC and AMT. Coughlin CR 2nd Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 27362913
Biochemical and molecular predictors for prognosis in nonketotic hyperglycinemia. Swanson MA Annals of neurology 2015 PMID: 26179960
Genetic heterogeneity of the GLDC gene in 28 unrelated patients with glycine encephalopathy. Conter C Journal of inherited metabolic disease 2006 PMID: 16601880

Text-mined citations for rs191905539...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021