BHMT2

betaine--homocysteine S-methyltransferase 2, the group of Homocysteine methyltransferases

Basic information

Region (hg38): 5:79069766-79090069

Links

ENSG00000132840 ∙ NCBI:23743 ∙ OMIM:605932 ∙ HGNC:1048 ∙ Uniprot:Q9H2M3 ∙ 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 BHMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BHMT2 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			27	1	1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	1

Variants in BHMT2

This is a list of pathogenic ClinVar variants found in the BHMT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-79069802-C-T		not specified	Uncertain significance (Sep 12, 2023)
5-79077485-T-G		not specified	Uncertain significance (Sep 25, 2023)
5-79077493-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-79077498-G-A		not specified	Uncertain significance (Jan 30, 2024)
5-79077570-G-C		not specified	Uncertain significance (Feb 22, 2023)
5-79077595-T-C		not specified	Uncertain significance (Feb 05, 2024)
5-79079371-C-T		not specified	Uncertain significance (Jan 23, 2024)
5-79079376-A-G			Likely benign (Dec 31, 2019)
5-79079378-T-G		not specified	Uncertain significance (Nov 06, 2023)
5-79079391-C-G		not specified	Uncertain significance (Feb 06, 2023)
5-79079399-C-T			Benign (Jul 13, 2018)
5-79080760-G-T		not specified	Uncertain significance (Aug 12, 2021)
5-79080790-A-G		not specified	Uncertain significance (Dec 01, 2022)
5-79080805-C-G		not specified	Uncertain significance (Jan 27, 2022)
5-79082834-T-C		not specified	Uncertain significance (Jan 09, 2024)
5-79082864-A-G		not specified	Likely benign (Jan 19, 2024)
5-79082885-T-C		not specified	Uncertain significance (Aug 02, 2021)
5-79082905-G-C		not specified	Uncertain significance (Jun 23, 2023)
5-79082926-G-A		not specified	Uncertain significance (Dec 07, 2021)
5-79083219-G-A		not specified	Uncertain significance (Jan 09, 2024)
5-79083258-T-C		not specified	Uncertain significance (Jul 15, 2021)
5-79083291-C-T		not specified	Uncertain significance (Jan 27, 2022)
5-79083324-C-T		not specified	Uncertain significance (Apr 06, 2022)
5-79083357-T-A		not specified	Uncertain significance (Apr 20, 2023)
5-79083640-G-T		not specified	Uncertain significance (Apr 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BHMT2	protein_coding	protein_coding	ENST00000255192	8	19750

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-15	0.00405	125318	1	429	125748	0.00171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.680	177	204	0.866	0.0000106	2365
Missense in Polyphen		57	63.16	0.90247		744
Synonymous	0.463	71	76.1	0.932	0.00000455	690
Loss of Function	-0.578	21	18.3	1.15	9.02e-7	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0123	0.0123
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000509	0.000489
Finnish	0.00172	0.00171
European (Non-Finnish)	0.000771	0.000765
Middle Eastern	0.000509	0.000489
South Asian	0.00216	0.00216
Other	0.00199	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of homocysteine metabolism. Converts homocysteine to methionine using S-methylmethionine (SMM) as a methyl donor. {ECO:0000269|PubMed:18230605}.
• Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Allograft Rejection;One carbon metabolism and related pathways;Metabolism of amino acids and derivatives;Metabolism;methionine salvage;Sulfur amino acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.977
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.0554
• hipred: N
• hipred_score: 0.195
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0515

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bhmt2

Gene ontology

• Biological process: sulfur amino acid metabolic process;amino-acid betaine metabolic process;methylation;S-methylmethionine metabolic process;S-adenosylmethionine metabolic process;L-methionine salvage
• Cellular component: cytosol;extracellular exosome
• Molecular function: zinc ion binding;betaine-homocysteine S-methyltransferase activity;S-methylmethionine-homocysteine S-methyltransferase activity