BHMT2
Basic information
Region (hg38): 5:79069767-79090069
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 27 | 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) | |||
5-79080720-G-A | not specified | Uncertain significance (Mar 19, 2024) | ||
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) | ||
5-79082822-T-A | not specified | Uncertain significance (May 20, 2024) | ||
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) |
GnomAD
Source:
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:
- 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
- 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