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NM_152783.5(D2HGDH):c.423C>T (p.Pro141=)

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Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Sep 24, 2020
Accession:
VCV000158419.6
Variation ID:
158419
Description:
single nucleotide variant
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NM_152783.5(D2HGDH):c.423C>T (p.Pro141=)

Allele ID
168060
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 241742507 (GRCh38) GRCh38 UCSC
2: 242681922 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.242681922C>T
NC_000002.12:g.241742507C>T
NG_012012.1:g.12893C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000002.12:241742506:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00060 (T)

Allele frequency
1000 Genomes Project 0.00060
The Genome Aggregation Database (gnomAD) 0.00140
The Genome Aggregation Database (gnomAD), exomes 0.00180
Trans-Omics for Precision Medicine (TOPMed) 0.00185
Exome Aggregation Consortium (ExAC) 0.00191
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00231
Links
ClinGen: CA171837
dbSNP: rs142473303
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 2 criteria provided, multiple submitters, no conflicts Sep 24, 2020 RCV000648997.5
Likely benign 1 criteria provided, single submitter Mar 17, 2014 RCV000145800.1
Uncertain significance 1 criteria provided, single submitter Jun 14, 2016 RCV000278547.3
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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
217 330

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Mar 17, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192937.1
Submitted: (Sep 11, 2014)
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (more)
Evidence details
Uncertain significance
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
D-2-Hydroxyglutaric Aciduria
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000429394.2
Submitted: (Oct 18, 2016)
Evidence details
Likely 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: SCV000429392.3
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
(Sep 24, 2020)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: germline
Invitae
Accession: SCV000770818.4
Submitted: (Jan 07, 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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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 rs142473303...

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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 29, 2021