BPNT1
Basic information
Region (hg38): 1:220057482-220090462
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 BPNT1 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 | 0 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in BPNT1
This is a list of pathogenic ClinVar variants found in the BPNT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-220059731-T-C | not specified | Uncertain significance (Dec 05, 2022) | ||
| 1-220062779-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 1-220062792-C-T | Likely benign (May 01, 2022) | |||
| 1-220062846-T-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-220062900-C-T | not specified | Uncertain significance (Apr 11, 2023) | ||
| 1-220067322-G-T | not specified | Uncertain significance (Mar 24, 2023) | ||
| 1-220067366-A-G | not specified | Uncertain significance (Mar 31, 2024) | ||
| 1-220067373-C-A | not specified | Uncertain significance (Aug 26, 2024) | ||
| 1-220072923-A-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-220074004-G-A | not specified | Uncertain significance (Aug 08, 2023) | ||
| 1-220074024-C-T | not specified | Uncertain significance (Nov 09, 2022) | ||
| 1-220074037-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
| 1-220074070-G-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 1-220079764-C-T | not specified | Uncertain significance (Aug 04, 2024) | ||
| 1-220079794-A-G | not specified | Uncertain significance (Dec 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BPNT1 | protein_coding | protein_coding | ENST00000469520 | 8 | 32981 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000223 | 0.915 | 124772 | 0 | 22 | 124794 | 0.0000881 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 119 | 169 | 0.706 | 0.00000850 | 1982 |
| Missense in Polyphen | 49 | 71.106 | 0.68911 | 822 | ||
| Synonymous | 0.389 | 56 | 59.8 | 0.936 | 0.00000292 | 617 |
| Loss of Function | 1.62 | 10 | 17.2 | 0.580 | 9.65e-7 | 198 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000190 | 0.000190 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000556 | 0.0000556 |
| Finnish | 0.0000464 | 0.0000464 |
| European (Non-Finnish) | 0.0000887 | 0.0000883 |
| Middle Eastern | 0.0000556 | 0.0000556 |
| South Asian | 0.000204 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Converts adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) and 3'(2')-phosphoadenosine 5'- phosphate (PAP) to AMP. Has 1000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2) and inositol 1,3,4- trisphosphate (Ins(1,3,4)P3), but does not hydrolyze Ins(1)P, Ins(3,4)P2, Ins(1,3,4,5)P4 or InsP6. {ECO:0000269|PubMed:10224133}.;
- Pathway
- Sulfur metabolism - Homo sapiens (human);Sulfate/Sulfite Metabolism;Sulfite oxidase deficiency;Phase II - Conjugation of compounds;Biological oxidations;Metabolism;Cytosolic sulfonation of small molecules
(Consensus)
Recessive Scores
- pRec
- 0.0964
Intolerance Scores
- loftool
- 0.657
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.28
Haploinsufficiency Scores
- pHI
- 0.187
- hipred
- N
- hipred_score
- 0.290
- ghis
- 0.407
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bpnt1
- Phenotype
- homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype;
Gene ontology
- Biological process
- nucleobase-containing compound metabolic process;nervous system development;dephosphorylation;phosphatidylinositol phosphorylation;3'-phosphoadenosine 5'-phosphosulfate metabolic process
- Cellular component
- cytosol
- Molecular function
- 3'(2'),5'-bisphosphate nucleotidase activity;metal ion binding