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GeneBe

BHMT

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

Basic information

Region (hg38): 5:79111808-79132288

Links

ENSG00000145692NCBI:635OMIM:602888HGNC:1047Uniprot:Q93088AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (19 variants)
  • not provided (4 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.

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
2
clinvar
21
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 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)2528362
5-79115845-T-A not specified Uncertain significance (Aug 22, 2023)2621481
5-79115848-G-A not specified Uncertain significance (Nov 14, 2023)3133824
5-79115854-G-C not specified Uncertain significance (Mar 21, 2023)2527605
5-79115893-G-A not specified Uncertain significance (Jul 13, 2021)2236526
5-79119261-C-T not specified Uncertain significance (Sep 15, 2021)2394965
5-79119262-G-T not specified Uncertain significance (Aug 04, 2023)2588019
5-79119274-G-A not specified Uncertain significance (Nov 29, 2021)2378491
5-79119276-G-C not specified Uncertain significance (Oct 26, 2021)2256817
5-79119304-T-A not specified Uncertain significance (Aug 17, 2021)2246044
5-79119314-C-T Benign (Aug 17, 2018)711926
5-79120416-G-A not specified Uncertain significance (Nov 09, 2022)2395493
5-79121227-C-T not specified Uncertain significance (Jul 05, 2023)2609424
5-79121329-C-T Benign (Aug 17, 2018)711927
5-79121335-G-A Benign (Jun 16, 2018)774306
5-79121350-C-T not specified Uncertain significance (Jan 10, 2022)2223865
5-79121356-G-C not specified Uncertain significance (May 16, 2022)2221415
5-79126048-G-A not specified Uncertain significance (May 15, 2023)2538019
5-79126069-T-G not specified Uncertain significance (Dec 08, 2023)3133826
5-79126120-G-T not specified Uncertain significance (Oct 20, 2023)3133827
5-79126168-G-T not specified Uncertain significance (Apr 28, 2022)2248630
5-79126187-G-A BHMT-related condition Likely benign (Jan 03, 2023)3036866
5-79127755-G-A not specified Uncertain significance (Mar 06, 2023)2454236
5-79127803-G-A not specified Uncertain significance (Jun 23, 2023)2601905
5-79127833-T-C not specified Uncertain significance (Oct 12, 2022)2392182

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BHMTprotein_codingprotein_codingENST00000274353 820507
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.74e-140.02281257000481257480.000191
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1472182240.9720.00001162634
Missense in Polyphen4954.9590.89158648
Synonymous1.286984.00.8220.00000479770
Loss of Function0.1172121.60.9730.00000111255

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005810.000575
Ashkenazi Jewish0.000.00
East Asian0.0004920.000489
Finnish0.00004620.0000462
European (Non-Finnish)0.0001680.000167
Middle Eastern0.0004920.000489
South Asian0.0002690.000229
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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