BHMT

betaine--homocysteine S-methyltransferase, the group of Homocysteine methyltransferases

Basic information

Region (hg38): 5:79111809-79132288

Links

ENSG00000145692 ∙ NCBI:635 ∙ OMIM:602888 ∙ HGNC:1047 ∙ Uniprot:Q93088 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	1
missense			28		2	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	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)
5-79115780-G-A		not specified	Uncertain significance (Nov 21, 2024)
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 (Oct 20, 2024)
5-79119276-G-C		not specified	Uncertain significance (Oct 26, 2021)
5-79119300-G-A		not specified	Uncertain significance (Dec 10, 2024)
5-79119304-T-A		not specified	Uncertain significance (Aug 17, 2021)
5-79119310-C-T		not specified	Uncertain significance (Oct 16, 2024)
5-79119314-C-T			Benign (Aug 17, 2018)
5-79120416-G-A		not specified	Uncertain significance (Nov 09, 2022)
5-79120440-C-T		not specified	Uncertain significance (Nov 27, 2024)
5-79120461-A-G		not specified	Uncertain significance (Apr 29, 2024)
5-79121227-C-T		not specified	Uncertain significance (Jul 05, 2023)
5-79121272-G-T		not specified	Uncertain significance (Oct 04, 2024)
5-79121300-T-G		not specified	Uncertain significance (Feb 26, 2025)
5-79121329-C-T			Benign (Aug 17, 2018)
5-79121335-G-A			Benign (Jun 16, 2018)
5-79121350-C-T		not specified	Uncertain significance (Jul 09, 2024)
5-79121356-G-C		not specified	Uncertain significance (May 16, 2022)
5-79126048-G-A		not specified	Uncertain significance (May 15, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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