L2HGDH, EX1-9DEL AND L-2-hydroxyglutaric aciduria

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 15, 2004
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000001678.4

Allele description [Variation Report for L2HGDH, EX1-9DEL]

L2HGDH, EX1-9DEL

Genes:

LOC130055566:ATAC-STARR-seq lymphoblastoid active region 8334 [Gene]
LOC130055568:ATAC-STARR-seq lymphoblastoid active region 8335 [Gene]
LOC130055569:ATAC-STARR-seq lymphoblastoid active region 8336 [Gene]
LOC130055572:ATAC-STARR-seq lymphoblastoid active region 8338 [Gene]
LOC130055573:ATAC-STARR-seq lymphoblastoid active region 8339 [Gene]
LOC130055574:ATAC-STARR-seq lymphoblastoid active region 8340 [Gene]
LOC130055575:ATAC-STARR-seq lymphoblastoid active region 8341 [Gene]
LOC130055576:ATAC-STARR-seq lymphoblastoid active region 8342 [Gene]
LOC130055577:ATAC-STARR-seq lymphoblastoid active region 8343 [Gene]
LOC130055578:ATAC-STARR-seq lymphoblastoid active region 8344 [Gene]
LOC130055579:ATAC-STARR-seq lymphoblastoid active region 8345 [Gene]
LOC130055580:ATAC-STARR-seq lymphoblastoid active region 8346 [Gene]
LOC130055581:ATAC-STARR-seq lymphoblastoid active region 8347 [Gene]
LOC130055582:ATAC-STARR-seq lymphoblastoid active region 8348 [Gene]
LOC130055583:ATAC-STARR-seq lymphoblastoid active region 8349 [Gene]
LOC130055584:ATAC-STARR-seq lymphoblastoid active region 8350 [Gene]
LOC130055585:ATAC-STARR-seq lymphoblastoid active region 8351 [Gene]
LOC130055586:ATAC-STARR-seq lymphoblastoid active region 8352 [Gene]
LOC130055587:ATAC-STARR-seq lymphoblastoid active region 8353 [Gene]
LOC130055589:ATAC-STARR-seq lymphoblastoid active region 8354 [Gene]
LOC130055567:ATAC-STARR-seq lymphoblastoid silent region 5714 [Gene]
LOC130055570:ATAC-STARR-seq lymphoblastoid silent region 5716 [Gene]
LOC130055571:ATAC-STARR-seq lymphoblastoid silent region 5717 [Gene]
LOC130055588:ATAC-STARR-seq lymphoblastoid silent region 5718 [Gene]
L2HGDH:L-2-hydroxyglutarate dehydrogenase [Gene - OMIM - HGNC]
LOC129390630:MPRA-validated peak2154 silencer [Gene]
SOS2:SOS Ras/Rho guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]
LOC125024480:Sharpr-MPRA regulatory region 10345 [Gene]
LOC125024479:Sharpr-MPRA regulatory region 12952 [Gene]
LINC01588:long intergenic non-protein coding RNA 1588 [Gene - HGNC]
LINC01599:long intergenic non-protein coding RNA 1599 [Gene - HGNC]
VCPKMT:valosin containing protein lysine methyltransferase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q21.3

Genomic location:

Chr14: 50000000 - 50247254 (on Assembly GRCh38)

Preferred name:

L2HGDH, EX1-9DEL

Other names:

L2HGDH, EX1-9DEL

HGVS:

NC_000014.9:g.(50000000_?)_(?_50247254)del

Note:

A deletion of several hundred kb, but retaining exon 10 of L2HGDH

Nucleotide change:

EX1-9 DEL

Links:

OMIM: 609584.0005

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000021834	OMIM	no assertion criteria provided	Pathogenic (Nov 15, 2004)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000021834

OMIM

no assertion criteria provided

Pathogenic
(Nov 15, 2004)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

L-2-Hydroxyglutaric aciduria: identification of a mutant gene C14orf160, localized on chromosome 14q22.1.

Topçu M, Jobard F, Halliez S, Coskun T, Yalçinkayal C, Gerceker FO, Wanders RJ, Prud'homme JF, Lathrop M, Ozguc M, Fischer J.

Hum Mol Genet. 2004 Nov 15;13(22):2803-11. Epub 2004 Sep 22.

PubMed [citation]

PMID:: 15385440

Details of each submission

From OMIM, SCV000021834.3

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

Description

In a child of a consanguineous Turkish family with L-2-hydroxyglutaric aciduria (L2HGA; 236792), Topcu et al. (2004) reported homozygosity for a large genomic deletion in the L2HGDH gene that eliminated exons 1 through 9.

#	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

Last Updated: Oct 14, 2023

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