LDHB
Basic information
Region (hg38): 12:21635342-21757857
Links
Phenotypes
GenCC
Source:
- glycogen storage disease due to lactate dehydrogenase H-subunit deficiency (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
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
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 | 7 | |||||
missense | 18 | 19 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region | 1 | 1 | ||||
non coding | 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 | Uncertain significance (Apr 27, 2017) | ||
12-21642032-C-T | Glycogen storage disease due to lactate dehydrogenase H-subunit deficiency | Affects (May 01, 1992) | ||
12-21642048-C-T | not specified | Uncertain significance (Sep 11, 2024) |
GnomAD
Source:
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:
- 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