BHMT
Basic information
Region (hg38): 5:79111808-79132288
Links
Phenotypes
GenCC
Source:
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 BHMT 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 | 1 | |||||
missense | 22 | 25 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 22 | 1 | 3 |
Variants in BHMT
This is a list of pathogenic ClinVar variants found in the BHMT region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
5-79111904-A-C | not specified | Uncertain significance (Mar 22, 2023) | ||
5-79115845-T-A | not specified | Uncertain significance (Aug 22, 2023) | ||
5-79115848-G-A | not specified | Uncertain significance (Nov 14, 2023) | ||
5-79115854-G-C | not specified | Uncertain significance (Mar 21, 2023) | ||
5-79115893-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
5-79119261-C-T | not specified | Uncertain significance (Sep 15, 2021) | ||
5-79119262-G-T | not specified | Uncertain significance (Aug 04, 2023) | ||
5-79119274-G-A | not specified | Uncertain significance (Nov 29, 2021) | ||
5-79119276-G-C | not specified | Uncertain significance (Oct 26, 2021) | ||
5-79119304-T-A | not specified | Uncertain significance (Aug 17, 2021) | ||
5-79119314-C-T | Benign (Aug 17, 2018) | |||
5-79120416-G-A | not specified | Uncertain significance (Nov 09, 2022) | ||
5-79120461-A-G | not specified | Uncertain significance (Apr 29, 2024) | ||
5-79121227-C-T | not specified | 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 | not specified | Uncertain significance (Jan 10, 2022) | ||
5-79121356-G-C | not specified | Uncertain significance (May 16, 2022) | ||
5-79126048-G-A | not specified | Uncertain significance (May 15, 2023) | ||
5-79126069-T-G | not specified | Uncertain significance (Dec 08, 2023) | ||
5-79126120-G-T | not specified | Uncertain significance (Oct 20, 2023) | ||
5-79126168-G-T | not specified | Uncertain significance (May 02, 2024) | ||
5-79126187-G-A | BHMT-related disorder | Likely benign (Jan 03, 2023) | ||
5-79127755-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
5-79127803-G-A | not specified | Uncertain significance (Jun 23, 2023) |
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