LDHB

lactate dehydrogenase B

Basic information

Region (hg38): 12:21635341-21757857

Links

ENSG00000111716 ∙ NCBI:3945 ∙ OMIM:150100 ∙ HGNC:6541 ∙ Uniprot:P07195 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• glycogen storage disease due to lactate dehydrogenase H-subunit deficiency (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lactate dehydrogenase B deficiency	AR	General	The clinical significance is unclear	Biochemical	5119336; 6383647; 2334429; 70259; 10509905; 11509017

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDHB 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			4	2	1	7
missense			18	1		19
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region			1			1
non coding			5		3	8
Total	0	0	28	4	4

Variants in LDHB

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

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

Position	Type	Phenotype	Significance	ClinVar
12-21635469-A-G		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21635574-A-G		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Affects (Sep 01, 1999)
12-21635601-G-A		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Apr 28, 2017)
12-21635637-C-T		not specified	Uncertain significance (Apr 05, 2023)
12-21635668-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Benign (Sep 19, 2018)
12-21635670-G-C		not specified	Uncertain significance (May 18, 2023)
12-21635704-C-T		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21635708-C-T		not specified	Uncertain significance (Aug 17, 2021)
12-21637082-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Mar 02, 2018)
12-21637115-A-C		not specified	Uncertain significance (Jan 09, 2024)
12-21637126-A-G		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21637141-C-T		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Apr 27, 2017)
12-21637150-A-G		not specified	Uncertain significance (Mar 25, 2024)
12-21637159-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency • not specified	Uncertain significance (Feb 01, 2023)
12-21637181-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 12, 2018)
12-21637182-G-A			Likely benign (May 21, 2018)
12-21637189-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21638338-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Benign (Jan 13, 2018)
12-21638445-C-A		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 12, 2018)
12-21641962-G-A		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21641990-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-21642019-A-T		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Uncertain significance (Jan 13, 2018)
12-21642024-T-C		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency • LDHB-related disorder	Conflicting classifications of pathogenicity (Oct 28, 2019)
12-21642032-C-T		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency	Affects (May 01, 1992)
12-21642075-G-A		Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency • LDHB-related disorder	Likely benign (Aug 31, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDHB	protein_coding	protein_coding	ENST00000396076	7	122516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000497	0.665	123796	72	1880	125748	0.00779

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.913	149	184	0.811	0.00000949	2204
Missense in Polyphen		19	43.358	0.43822		647
Synonymous	0.783	58	66.1	0.877	0.00000356	641
Loss of Function	1.01	10	14.1	0.710	5.94e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0533	0.0533
Ashkenazi Jewish	0.00	0.00
East Asian	0.00685	0.00687
Finnish	0.00	0.00
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.00685	0.00687
South Asian	0.000623	0.000621
Other	0.00702	0.00686

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Lactate dehydrogenase B deficiency (LDHBD) [MIM:614128]: A condition with no deleterious effects on health. LDHBD is of interest to laboratory medicine mainly because it can cause misdiagnosis in those disorders in which elevation of serum LDH is expected. {ECO:0000269|PubMed:10211631, ECO:0000269|PubMed:11509017, ECO:0000269|PubMed:1587525, ECO:0000269|PubMed:2334429, ECO:0000269|PubMed:8314553, ECO:0000269|PubMed:8462975, ECO:0000269|PubMed:8611651, ECO:0000269|PubMed:9929983, ECO:0000269|Ref.20}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Pyruvate metabolism - Homo sapiens (human);Glycolysis / Gluconeogenesis - Homo sapiens (human);Propanoate metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Pathways in clear cell renal cell carcinoma;Glycolysis and Gluconeogenesis;Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;Glycolysis Gluconeogenesis;lactate fermentation (reoxidation of cytosolic NADH);The citric acid (TCA) cycle and respiratory electron transport;TCR;Metabolism;Methionine Cysteine metabolism;Propanoate metabolism;Pyruvate metabolism (Consensus)

Recessive Scores

• pRec: 0.851

Intolerance Scores

• loftool: 0.331
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.549
• hipred: Y
• hipred_score: 0.562
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ldhb
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: carbohydrate metabolic process;pyruvate metabolic process;oxidation-reduction process
• Cellular component: cytoplasm;cytosol;membrane;membrane raft;extracellular exosome
• Molecular function: L-lactate dehydrogenase activity;protein binding;identical protein binding