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NM_000170.3(GLDC):c.2053-5C>G

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(2);Likely benign(4);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
9 (Most recent: Sep 23, 2021)
Last evaluated:
Apr 1, 2021
Accession:
VCV000235561.16
Variation ID:
235561
Description:
single nucleotide variant
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NM_000170.3(GLDC):c.2053-5C>G

Allele ID
237242
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.1
Genomic location
9: 6556307 (GRCh38) GRCh38 UCSC
9: 6556307 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.6556307G>C
NG_016397.1:g.94386C>G
NM_000170.3:c.2053-5C>G MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:6556306:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00120 (C)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00220
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00315
1000 Genomes Project 0.00120
Trans-Omics for Precision Medicine (TOPMed) 0.00264
The Genome Aggregation Database (gnomAD) 0.00278
Exome Aggregation Consortium (ExAC) 0.00221
Trans-Omics for Precision Medicine (TOPMed) 0.00310
Links
ClinGen: CA4980404
dbSNP: rs140877566
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 28, 2020 RCV000552095.6
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Apr 1, 2021 RCV000223973.11
Benign 1 no assertion criteria provided - RCV001701793.1
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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
Uncertain Significance
(Mar 22, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000281240.1
Submitted: (May 19, 2016)
Evidence details
Comment:
Converted during submission to Uncertain significance.
Benign
(Nov 28, 2020)
criteria provided, single submitter
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: germline
Invitae
Accession: SCV000636373.5
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(May 16, 2018)
criteria provided, single submitter
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: unknown
Counsyl
Accession: SCV000799995.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Non-ketotic hyperglycinemia
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001331902.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 03, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV001475874.1
Submitted: (Dec 30, 2020)
Evidence details
Publications
PubMed (1)
Likely benign
(Aug 21, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001795794.1
Submitted: (Aug 19, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28244183)
Likely benign
(Apr 01, 2021)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001155601.7
Submitted: (Jul 04, 2021)
Evidence details
Benign
(-)
no assertion criteria provided
Method: clinical testing
not specified
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001930466.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001966042.1
Submitted: (Sep 21, 2021)
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
Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease. Bravo-Alonso I Human mutation 2017 PMID: 28244183

Text-mined citations for rs140877566...

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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