BHMT
Basic information
Region (hg38): 5:79111809-79132288
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
- not_provided (4 variants)
- BHMT-related_disorder (1 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. These statistics are base on transcript: NM_000001713.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 41 | 45 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 42 | 2 | 3 |
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