PLA2G12B
Basic information
Region (hg38): 10:72934761-72954806
Previous symbols: [ "PLA2G13" ]
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 PLA2G12B 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 | 10 | ||||
| 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 | 0 | 0 |
Variants in PLA2G12B
This is a list of pathogenic ClinVar variants found in the PLA2G12B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-72935645-C-T | not specified | Uncertain significance (Nov 15, 2023) | ||
| 10-72935694-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 10-72935700-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 10-72935714-G-T | not specified | Uncertain significance (May 20, 2024) | ||
| 10-72941219-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 10-72941228-C-A | not specified | Uncertain significance (Feb 21, 2024) | ||
| 10-72942660-G-A | not specified | Uncertain significance (Dec 13, 2022) | ||
| 10-72942687-C-T | not specified | Likely benign (May 13, 2024) | ||
| 10-72942690-A-G | not specified | Uncertain significance (Sep 17, 2021) | ||
| 10-72954576-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 10-72954603-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
| 10-72954614-G-C | not specified | Uncertain significance (Apr 22, 2022) | ||
| 10-72954618-G-A | not specified | Uncertain significance (Feb 05, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLA2G12B | protein_coding | protein_coding | ENST00000373032 | 4 | 19609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000954 | 0.822 | 125727 | 0 | 20 | 125747 | 0.0000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.654 | 95 | 115 | 0.828 | 0.00000681 | 1269 |
| Missense in Polyphen | 25 | 46.03 | 0.54313 | 489 | ||
| Synonymous | 1.33 | 33 | 44.3 | 0.745 | 0.00000257 | 373 |
| Loss of Function | 1.16 | 6 | 9.93 | 0.604 | 5.93e-7 | 108 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000173 | 0.000173 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000798 | 0.0000791 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000134 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Not known; does not seem to have catalytic activity.;
- Pathway
- Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Ras Signaling;Linoleate metabolism;Glycerophospholipid metabolism;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.492
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.483
- hipred
- N
- hipred_score
- 0.444
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.559
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pla2g12b
- Phenotype
- liver/biliary system phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- pla2g12b
- Affected structure
- yolk
- Phenotype tag
- abnormal
- Phenotype quality
- color
Gene ontology
- Biological process
- phospholipid metabolic process;lipid catabolic process;arachidonic acid secretion
- Cellular component
- extracellular region
- Molecular function
- phospholipase A2 activity;calcium ion binding