BHMT
betaine--homocysteine S-methyltransferase, the group of Homocysteine methyltransferases
Basic information
Region (hg38): 5:79111808-79132288
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (11 variants)
- not provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BHMT gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 11 | 2 | 13 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 3 |
Variants in BHMT
This is a list of pathogenic ClinVar variants found in the BHMT region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-79111904-A-C | Inborn genetic diseases | Uncertain significance (Mar 22, 2023) | ||
| 5-79115845-T-A | Inborn genetic diseases | Uncertain significance (Aug 22, 2023) | ||
| 5-79115854-G-C | Inborn genetic diseases | Uncertain significance (Mar 21, 2023) | ||
| 5-79115893-G-A | Inborn genetic diseases | Uncertain significance (Jul 13, 2021) | ||
| 5-79119261-C-T | Inborn genetic diseases | Uncertain significance (Sep 15, 2021) | ||
| 5-79119262-G-T | Inborn genetic diseases | Uncertain significance (Aug 04, 2023) | ||
| 5-79119274-G-A | Inborn genetic diseases | Uncertain significance (Nov 29, 2021) | ||
| 5-79119276-G-C | Inborn genetic diseases | Uncertain significance (Oct 26, 2021) | ||
| 5-79119304-T-A | Inborn genetic diseases | Uncertain significance (Aug 17, 2021) | ||
| 5-79119314-C-T | Benign (Aug 17, 2018) | |||
| 5-79120416-G-A | Inborn genetic diseases | Uncertain significance (Nov 09, 2022) | ||
| 5-79121227-C-T | Inborn genetic diseases | Uncertain significance (Jul 05, 2023) | ||
| 5-79121329-C-T | Benign (Aug 17, 2018) | |||
| 5-79121335-G-A | Benign (Jun 16, 2018) | |||
| 5-79121350-C-T | Inborn genetic diseases | Uncertain significance (Jan 10, 2022) | ||
| 5-79121356-G-C | Inborn genetic diseases | Uncertain significance (May 16, 2022) | ||
| 5-79126048-G-A | Inborn genetic diseases | Uncertain significance (May 15, 2023) | ||
| 5-79126168-G-T | Inborn genetic diseases | Uncertain significance (Apr 28, 2022) | ||
| 5-79127755-G-A | Inborn genetic diseases | Uncertain significance (Mar 06, 2023) | ||
| 5-79127803-G-A | Inborn genetic diseases | Uncertain significance (Jun 23, 2023) | ||
| 5-79127833-T-C | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
| 5-79131036-G-A | Inborn genetic diseases | Uncertain significance (Apr 13, 2022) | ||
| 5-79131090-GA-G | not provided (-) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BHMT | protein_coding | protein_coding | ENST00000274353 | 8 | 20507 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.74e-14 | 0.0228 | 125700 | 0 | 48 | 125748 | 0.000191 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.147 | 218 | 224 | 0.972 | 0.0000116 | 2634 |
| Missense in Polyphen | 49 | 54.959 | 0.89158 | 648 | ||
| Synonymous | 1.28 | 69 | 84.0 | 0.822 | 0.00000479 | 770 |
| Loss of Function | 0.117 | 21 | 21.6 | 0.973 | 0.00000111 | 255 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000581 | 0.000575 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000492 | 0.000489 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000168 | 0.000167 |
| Middle Eastern | 0.000492 | 0.000489 |
| South Asian | 0.000269 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the regulation of homocysteine metabolism. Converts betaine and homocysteine to dimethylglycine and methionine, respectively. This reaction is also required for the irreversible oxidation of choline.;
- Pathway
- Cysteine and methionine metabolism - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;3-Phosphoglycerate dehydrogenase deficiency;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Non Ketotic Hyperglycinemia;Glycine and Serine Metabolism;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Betaine Metabolism;Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;sarcosine oncometabolite pathway ;Dimethylglycine Dehydrogenase Deficiency;Hyperglycinemia, non-ketotic;Dimethylglycine Dehydrogenase Deficiency;Sarcosinemia;Cystathionine Beta-Synthase Deficiency;Dihydropyrimidine Dehydrogenase Deficiency (DHPD);One Carbon Metabolism;Trans-sulfuration and one carbon metabolism;Methionine De Novo and Salvage Pathway;Amino Acid metabolism;One carbon metabolism and related pathways;Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;Choline catabolism;Methionine Cysteine metabolism;glycine betaine degradation;methionine salvage;superpathway of choline degradation to L-serine;Sulfur amino acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.225
Intolerance Scores
- loftool
- 0.850
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.22
Haploinsufficiency Scores
- pHI
- 0.111
- hipred
- N
- hipred_score
- 0.226
- ghis
- 0.446
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.813
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bhmt
- Phenotype
- renal/urinary system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- bhmt
- Affected structure
- pancreatic B cell
- Phenotype tag
- abnormal
- Phenotype quality
- increased amount
Gene ontology
- Biological process
- sulfur amino acid metabolic process;protein methylation;amino-acid betaine metabolic process;amino-acid betaine catabolic process;choline catabolic process;S-adenosylmethionine metabolic process;regulation of homocysteine metabolic process;L-methionine salvage
- Cellular component
- cytosol;extracellular exosome
- Molecular function
- zinc ion binding;betaine-homocysteine S-methyltransferase activity