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NM_152783.5(D2HGDH):c.1063G>A (p.Gly355Ser)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 31, 2019
Accession:
VCV000210810.6
Variation ID:
210810
Description:
single nucleotide variant
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NM_152783.5(D2HGDH):c.1063G>A (p.Gly355Ser)

Allele ID
206987
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 241751311 (GRCh38) GRCh38 UCSC
2: 242690726 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.242690726G>A
NC_000002.12:g.241751311G>A
NG_012012.1:g.21697G>A
... more HGVS
Protein change
G355S, G221S, G168S
Other names
-
Canonical SPDI
NC_000002.12:241751310:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00939
Exome Aggregation Consortium (ExAC) 0.00948
1000 Genomes Project 0.00140
Trans-Omics for Precision Medicine (TOPMed) 0.00656
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00823
The Genome Aggregation Database (gnomAD) 0.01274
Links
ClinGen: CA207099
dbSNP: rs139321130
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Dec 31, 2019 RCV001084317.2
Likely benign 1 criteria provided, single submitter Jun 29, 2015 RCV000193545.2
Likely benign 1 criteria provided, single submitter Mar 9, 2017 RCV000514436.4
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
D2HGDH - - GRCh38
GRCh37
218 331

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 29, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000247144.1
Submitted: (Sep 15, 2015)
Evidence details
Likely benign
(Mar 09, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610678.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000429403.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: germline
Invitae
Accession: SCV001113667.2
Submitted: (Jan 29, 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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs139321130...

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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 Oct 30, 2021