OGDHL

oxoglutarate dehydrogenase L, the group of Oxoglutarate dehydrogenase family

Basic information

Region (hg38): 10:49734640-49762379

Links

ENSG00000197444 ∙ NCBI:55753 ∙ OMIM:617513 ∙ HGNC:25590 ∙ Uniprot:Q9ULD0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Yoon-Bellen neurodevelopmental syndrome (Moderate), mode of inheritance: AR
• Yoon-Bellen neurodevelopmental syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Yoon-Bellen neurodevelopmental syndrome	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	34800363

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OGDHL gene.

• Inborn genetic diseases (42 variants)
• not provided (14 variants)
• Yoon-Bellen neurodevelopmental syndrome (4 variants)
• Abnormal brain morphology (1 variants)
• OGDHL-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OGDHL gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	5	7
missense		2	42	5	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region				1		1
non coding					1	1
Total	0	3	42	7	7

Highest pathogenic variant AF is 0.0000460

Variants in OGDHL

This is a list of pathogenic ClinVar variants found in the OGDHL region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-49735277-A-C		Inborn genetic diseases	Uncertain significance (Dec 14, 2023)
10-49735293-C-G		Inborn genetic diseases	Uncertain significance (Jul 24, 2022)
10-49735330-C-T			Benign (Jun 26, 2018)
10-49736038-C-T		OGDHL-related disorder	Uncertain significance (Oct 30, 2022)
10-49736114-C-T		OGDHL-related disorder	Benign (Mar 04, 2019)
10-49736122-G-A		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
10-49736369-C-T		OGDHL-related disorder	Likely benign (Nov 16, 2019)
10-49736444-G-A		OGDHL-related disorder	Likely benign (Dec 31, 2019)
10-49736471-G-A		OGDHL-related disorder	Likely benign (Mar 22, 2019)
10-49736482-C-A		OGDHL-related disorder	Likely benign (Jul 19, 2022)
10-49736483-G-A		OGDHL-related disorder	Benign (Mar 27, 2019)
10-49736484-G-A		Inborn genetic diseases	Uncertain significance (Jun 13, 2022)
10-49736505-C-T		Inborn genetic diseases	Uncertain significance (Aug 30, 2022)
10-49737822-G-C		Yoon-Bellen neurodevelopmental syndrome	Pathogenic (Jan 14, 2022)
10-49737840-T-C		Inborn genetic diseases	Uncertain significance (Feb 03, 2022)
10-49737844-T-G		OGDHL-related disorder	Likely benign (Sep 25, 2019)
10-49738249-G-A		Abnormal brain morphology • Yoon-Bellen neurodevelopmental syndrome	Likely pathogenic (-)
10-49738261-C-T		Inborn genetic diseases	Uncertain significance (Jan 11, 2023)
10-49739680-G-A		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
10-49739684-G-T		Inborn genetic diseases	Uncertain significance (Nov 19, 2022)
10-49739707-C-T		Yoon-Bellen neurodevelopmental syndrome • Inborn genetic diseases	Uncertain significance (Aug 24, 2023)
10-49739708-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
10-49739761-G-A		Inborn genetic diseases	Uncertain significance (May 16, 2022)
10-49739779-A-G		Inborn genetic diseases • OGDHL-related disorder	Benign/Likely benign (Jan 01, 2024)
10-49739798-C-T		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OGDHL	protein_coding	protein_coding	ENST00000374103	22	27737

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.69e-10	1.00	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.497	610	646	0.945	0.0000415	6649
Missense in Polyphen		209	227.95	0.91688		2224
Synonymous	-0.00647	261	261	1.00	0.0000170	1963
Loss of Function	3.29	23	47.5	0.484	0.00000212	544

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000610	0.000598
Middle Eastern	0.000326	0.000326
South Asian	0.000328	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Citrate cycle (TCA cycle) - Homo sapiens (human);Tryptophan metabolism - Homo sapiens (human);Lysine degradation - Homo sapiens (human);Lysine metabolism;TCA cycle (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.0661
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.03

Haploinsufficiency Scores

• pHI: 0.383
• hipred: Y
• hipred_score: 0.738
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.600

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ogdhl

Gene ontology

• Biological process: glycolytic process;tricarboxylic acid cycle
• Cellular component: mitochondrion;mitochondrial matrix;oxoglutarate dehydrogenase complex
• Molecular function: oxoglutarate dehydrogenase (succinyl-transferring) activity;protein binding;thiamine pyrophosphate binding;metal ion binding