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NM_024884.3(L2HGDH):c.1003C>T (p.Arg335Ter) AND L-2-hydroxyglutaric aciduria

Germline classification:
Pathogenic (2 submissions)
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000023778.9

Allele description [Variation Report for NM_024884.3(L2HGDH):c.1003C>T (p.Arg335Ter)]

NM_024884.3(L2HGDH):c.1003C>T (p.Arg335Ter)

Gene:
L2HGDH:L-2-hydroxyglutarate dehydrogenase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q21.3
Genomic location:
Preferred name:
NM_024884.3(L2HGDH):c.1003C>T (p.Arg335Ter)
Other names:
L2HGDH, ARG335TER
HGVS:
  • NC_000014.9:g.50267814G>A
  • NG_008092.1:g.49416C>T
  • NM_024884.3:c.1003C>TMANE SELECT
  • NP_079160.1:p.Arg335Ter
  • NC_000014.8:g.50734532G>A
  • p.(Arg335Ter)
Protein change:
R335*; ARG335TER
Links:
OMIM: 609584.0007; dbSNP: rs387907013
NCBI 1000 Genomes Browser:
rs387907013
Molecular consequence:
  • NM_024884.3:c.1003C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

Name:
L-2-hydroxyglutaric aciduria (L2HGA)
Identifiers:
MONDO: MONDO:0009370; MedGen: C1855995; Orphanet: 79314; OMIM: 236792; Human Phenotype Ontology: HP:0040144

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Assertion and evidence details

Help
Submission Accession Submitter Review Status
(Assertion method)		 Clinical Significance
(Last evaluated)		 Origin Method Citations
SCV000045069 OMIM
no assertion criteria provided
Pathogenic
(Sep 21, 2011)		 germline literature only

PubMed (1)
[See all records that cite this PMID]
SCV001482024 Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn
criteria provided, single submitter

(ACMG Guidelines, 2015)		 Pathogenic germline clinical testing

PubMed (1)
[See all records that cite this PMID]
Help

Summary from all submissions

Ethnicity Origin Affected Individuals Families Chromosomes tested Number Tested Family history Method
not provided germline yes 1 not provided not provided not provided not provided clinical testing
not provided germline not provided not provided not provided not provided not provided not provided literature only

Citations

PubMed

Deep sequencing reveals 50 novel genes for recessive cognitive disorders.

Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P, Zecha A, Mohseni M, Püttmann L, Vahid LN, Jensen C, Moheb LA, Bienek M, Larti F, Mueller I, Weissmann R, Darvish H, Wrogemann K, et al.

Nature. 2011 Sep 21;478(7367):57-63. doi: 10.1038/nature10423.

PubMed [citation]
PMID:
21937992

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000045069.5

# Ethnicity Individuals Chromosomes Tested Family History Method Citations
1 not provided not provided not provided not provided literature only PubMed (1)

Description

Najmabadi et al. (2011) identified a family (8600276) in which 4 of 7 children of distantly related parents had L-2-hydroxyglutaric aciduria (L2HGA; 236792) and profound intellectual disability. Affected individuals were homozygous for a G-to-A transition at genomic coordinate chr14:49,804,282 (NCBI36), resulting in an arg335-to-ter (R335X) substitution. Both parents were carriers.

# Sample Method Observation
Origin Affected Number tested Tissue Purpose Method Individuals Allele frequency Families Co-occurrences
1 germline not provided not provided not provided not provided not provided not provided not provided not provided

From Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, SCV001482024.1

# Ethnicity Individuals Chromosomes Tested Family History Method Citations
1 1 not provided not provided clinical testing PubMed (1)

Description

ACMG classificatio: class 5 (PVS1, PM2, PP5)

# Sample Method Observation
Origin Affected Number tested Tissue Purpose Method Individuals Allele frequency Families Co-occurrences
1 germline yes not provided not provided not provided 1 not provided not provided not provided

Last Updated: Mar 4, 2023