Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

NM_152783.5(D2HGDH):c.1276G>A (p.Ala426Thr)

Help
Interpretation:
Conflicting interpretations of pathogenicity​

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

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 17, 2020
Accession:
VCV000158410.15
Variation ID:
158410
Description:
single nucleotide variant
Help

NM_152783.5(D2HGDH):c.1276G>A (p.Ala426Thr)

Allele ID
168070
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q37.3
Genomic location
2: 241755984 (GRCh38) GRCh38 UCSC
2: 242695399 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.242695399G>A
NC_000002.12:g.241755984G>A
NG_012012.1:g.26370G>A
... more HGVS
Protein change
A426T, A292T, A239T
Other names
-
Canonical SPDI
NC_000002.12:241755983:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00409
Exome Aggregation Consortium (ExAC) 0.00729
The Genome Aggregation Database (gnomAD) 0.00782
1000 Genomes Project 0.00200
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00554
The Genome Aggregation Database (gnomAD), exomes 0.00710
Links
ClinGen: CA171824
dbSNP: rs146578303
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 2 criteria provided, multiple submitters, no conflicts Jul 17, 2017 RCV000145791.4
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Nov 17, 2020 RCV000987080.4
Conflicting interpretations of pathogenicity 5 criteria provided, conflicting interpretations Sep 1, 2016 RCV000444247.8
Help
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

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jul 17, 2017)
criteria provided, single submitter
Method: clinical testing
Not Specified
Allele origin: germline
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital
Accession: SCV000864338.1
Submitted: (Dec 14, 2018)
Evidence details
Comment:
BS1, BP6; This alteration has an allele frequency that is greater than expected for the associated disease, and was reported as a benign/likely benign alteration … (more)
Benign
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: germline
Invitae
Accession: SCV001107582.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 28, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000192928.2
Submitted: (Sep 15, 2015)
Evidence details
Likely Benign
(Jul 07, 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: SCV000510958.1
Submitted: (Feb 17, 2017)
Evidence details
Comment:
Converted during submission to Likely benign.
Benign
(May 28, 2019)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: unknown
Mendelics
Accession: SCV001136278.1
Submitted: (Oct 22, 2019)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
D-2-hydroxyglutaric aciduria 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000429412.3
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)
Uncertain significance
(Sep 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001153393.7
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Feb 23, 2016)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: unknown
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV000802845.1
Submitted: (May 23, 2018)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
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: SCV001931583.1
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: SCV001966728.1
Submitted: (Sep 21, 2021)
Evidence details

Functional evidence

Help
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

Help
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 rs146578303...

Help
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 07, 2021