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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:Q93088AlphaFoldGenCCjaxSfariGnomADPubmed

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 (11 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 1
missense 11 2 13
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 0 0 11 0 3

Variants in BHMT

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

Position Type Phenotype Significance ClinVar
5-79111904-A-C Inborn genetic diseases Uncertain significance (Mar 22, 2023)link
5-79115845-T-A Inborn genetic diseases Uncertain significance (Aug 22, 2023)link
5-79115854-G-C Inborn genetic diseases Uncertain significance (Mar 21, 2023)link
5-79115893-G-A Inborn genetic diseases Uncertain significance (Jul 13, 2021)link
5-79119261-C-T Inborn genetic diseases Uncertain significance (Sep 15, 2021)link
5-79119262-G-T Inborn genetic diseases Uncertain significance (Aug 04, 2023)link
5-79119274-G-A Inborn genetic diseases Uncertain significance (Nov 29, 2021)link
5-79119276-G-C Inborn genetic diseases Uncertain significance (Oct 26, 2021)link
5-79119304-T-A Inborn genetic diseases Uncertain significance (Aug 17, 2021)link
5-79119314-C-T Benign (Aug 17, 2018)link
5-79120416-G-A Inborn genetic diseases Uncertain significance (Nov 09, 2022)link
5-79121227-C-T Inborn genetic diseases Uncertain significance (Jul 05, 2023)link
5-79121329-C-T Benign (Aug 17, 2018)link
5-79121335-G-A Benign (Jun 16, 2018)link
5-79121350-C-T Inborn genetic diseases Uncertain significance (Jan 10, 2022)link
5-79121356-G-C Inborn genetic diseases Uncertain significance (May 16, 2022)link
5-79126048-G-A Inborn genetic diseases Uncertain significance (May 15, 2023)link
5-79126168-G-T Inborn genetic diseases Uncertain significance (Apr 28, 2022)link
5-79127755-G-A Inborn genetic diseases Uncertain significance (Mar 06, 2023)link
5-79127803-G-A Inborn genetic diseases Uncertain significance (Jun 23, 2023)link
5-79127833-T-C Inborn genetic diseases Uncertain significance (Oct 12, 2022)link
5-79131036-G-A Inborn genetic diseases Uncertain significance (Apr 13, 2022)link
5-79131090-GA-G not provided (-)link

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