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GeneBe

BHMT2

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

Basic information

Region (hg38): 5:79069766-79090069

Links

ENSG00000132840NCBI:23743OMIM:605932HGNC:1048Uniprot:Q9H2M3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BHMT2 gene.

  • Inborn genetic diseases (19 variants)
  • not provided (2 variants)

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
clinvar
1
missense
19
clinvar
1
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 19 1 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)2622485
5-79077485-T-G not specified Uncertain significance (Sep 25, 2023)3133831
5-79077493-G-A not specified Uncertain significance (Aug 16, 2021)2393330
5-79077498-G-A not specified Uncertain significance (Jan 30, 2024)3133834
5-79077570-G-C not specified Uncertain significance (Feb 22, 2023)2487706
5-79077595-T-C not specified Uncertain significance (Feb 05, 2024)3133828
5-79079371-C-T not specified Uncertain significance (Jan 23, 2024)3133829
5-79079376-A-G Likely benign (Dec 31, 2019)732484
5-79079378-T-G not specified Uncertain significance (Nov 06, 2023)3133830
5-79079391-C-G not specified Uncertain significance (Feb 06, 2023)2480982
5-79079399-C-T Benign (Jul 13, 2018)774305
5-79080760-G-T not specified Uncertain significance (Aug 12, 2021)2388866
5-79080790-A-G not specified Uncertain significance (Dec 01, 2022)2331252
5-79080805-C-G not specified Uncertain significance (Jan 27, 2022)2274490
5-79082834-T-C not specified Uncertain significance (Jan 09, 2024)3133832
5-79082864-A-G not specified Likely benign (Jan 19, 2024)3133833
5-79082885-T-C not specified Uncertain significance (Aug 02, 2021)2227293
5-79082905-G-C not specified Uncertain significance (Jun 23, 2023)2594394
5-79082926-G-A not specified Uncertain significance (Dec 07, 2021)3133835
5-79083219-G-A not specified Uncertain significance (Jan 09, 2024)2368729
5-79083258-T-C not specified Uncertain significance (Jul 15, 2021)2237850
5-79083291-C-T not specified Uncertain significance (Jan 27, 2022)2223942
5-79083324-C-T not specified Uncertain significance (Apr 06, 2022)2402889
5-79083357-T-A not specified Uncertain significance (Apr 20, 2023)2525403
5-79083640-G-T not specified Uncertain significance (Apr 04, 2023)2532304

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BHMT2protein_codingprotein_codingENST00000255192 819750
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.96e-150.0040512531814291257480.00171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6801772040.8660.00001062365
Missense in Polyphen5763.160.90247744
Synonymous0.4637176.10.9320.00000455690
Loss of Function-0.5782118.31.159.02e-7220

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01230.0123
Ashkenazi Jewish0.00009930.0000992
East Asian0.0005090.000489
Finnish0.001720.00171
European (Non-Finnish)0.0007710.000765
Middle Eastern0.0005090.000489
South Asian0.002160.00216
Other0.001990.00196

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bhmt2
Phenotype

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