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NM_000159.4(GCDH):c.1173del (p.Asn392fs)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Feb 26, 2021)
Last evaluated:
Feb 1, 2021
Accession:
VCV000370106.4
Variation ID:
370106
Description:
1bp deletion
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NM_000159.4(GCDH):c.1173del (p.Asn392fs)

Allele ID
358603
Variant type
Deletion
Variant length
1 bp
Cytogenetic location
19p13.13
Genomic location
19: 12897787 (GRCh38) GRCh38 UCSC
19: 13008601 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NG_009292.1:g.11634delG
NC_000019.10:g.12897793del
NC_000019.9:g.13008607del
... more HGVS
Protein change
N392fs
Other names
-
Canonical SPDI
NC_000019.10:12897786:GGGGGGG:GGGGGG
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA9234625
dbSNP: rs754002357
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 4 criteria provided, multiple submitters, no conflicts Feb 1, 2021 RCV000410057.4
Likely pathogenic 1 criteria provided, single submitter Sep 28, 2018 RCV001008118.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
GCDH - - GRCh38
GRCh37
374 458

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Nov 19, 2015)
criteria provided, single submitter
Method: clinical testing
Glutaric aciduria, type 1
Allele origin: unknown
Counsyl
Accession: SCV000485337.1
Submitted: (Nov 23, 2016)
Evidence details
Publications
PubMed (2)
Pathogenic
(Feb 01, 2021)
criteria provided, single submitter
Method: clinical testing
Glutaric aciduria, type 1
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001482118.1
Submitted: (Feb 26, 2021)
Evidence details
Publications
PubMed (3)
Comment:
Variant summary: GCDH c.1173delG (p.Asn392MetfsX9) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Feb 26, 2018)
criteria provided, single submitter
Method: clinical testing
Glutaric aciduria, type 1
Allele origin: germline
Invitae
Accession: SCV000831180.1
Submitted: (Aug 29, 2018)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change results in a premature translational stop signal in the GCDH gene (p.Asn392Metfs*9). While this is not anticipated to result in nonsense mediated … (more)
Likely pathogenic
(Sep 28, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001167871.1
Submitted: (Oct 15, 2019)
Evidence details
Comment:
The c.1173delG variant has been published in patients with glutaric aciduria type 1 both in the homozygous state and with a second GCDH variant (Anikster … (more)
Likely pathogenic
(Jun 02, 2016)
no assertion criteria provided
Method: research
Glutaric aciduria, type 1
Allele origin: germline
National Institute of Mental Health and Neurosciences
Accession: SCV000897926.1
Submitted: (Jan 14, 2019)
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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Glutaric Acidemia Type 1-Clinico-Molecular Profile and Novel Mutations in GCDH Gene in Indian Patients. Gupta N JIMD reports 2015 PMID: 25762492
Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct. Busquets C Pediatric research 2000 PMID: 10960496
Glutaric aciduria type I in the Arab and Jewish communities in Israel. Anikster Y American journal of human genetics 1996 PMID: 8900228

Text-mined citations for rs754002357...

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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 Sep 18, 2021