LYPLA2
Basic information
Region (hg38): 1:23791110-23795539
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 LYPLA2 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 | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 0 | 0 |
Variants in LYPLA2
This is a list of pathogenic ClinVar variants found in the LYPLA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-23792732-T-G | not specified | Uncertain significance (Aug 12, 2022) | ||
| 1-23792743-G-C | not specified | Uncertain significance (Jun 11, 2021) | ||
| 1-23792746-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 1-23793164-G-C | not specified | Uncertain significance (Jun 10, 2022) | ||
| 1-23793867-C-G | not specified | Uncertain significance (Dec 27, 2022) | ||
| 1-23793916-A-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 1-23794068-G-A | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-23794104-G-A | not specified | Uncertain significance (Jan 10, 2023) | ||
| 1-23794311-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
| 1-23794448-G-A | not specified | Uncertain significance (Nov 20, 2023) | ||
| 1-23794694-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 1-23794710-A-C | not specified | Uncertain significance (Dec 08, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LYPLA2 | protein_coding | protein_coding | ENST00000374514 | 9 | 4570 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.950 | 0.0504 | 125735 | 0 | 4 | 125739 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 88 | 146 | 0.604 | 0.00000860 | 1489 |
| Missense in Polyphen | 20 | 47.233 | 0.42343 | 552 | ||
| Synonymous | -0.310 | 62 | 59.0 | 1.05 | 0.00000376 | 479 |
| Loss of Function | 3.19 | 1 | 13.8 | 0.0724 | 7.52e-7 | 141 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000119 | 0.000119 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins such as trimeric G alpha proteins, GAP43, ZDHHC6 or HRAS (PubMed:21152083, PubMed:28826475). Deacylates GAP43 (PubMed:21152083). Mediates depalmitoylation of ZDHHC6 (PubMed:28826475). Has lysophospholipase activity (By similarity). {ECO:0000250|UniProtKB:Q9WTL7, ECO:0000269|PubMed:21152083, ECO:0000269|PubMed:28826475}.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Developmental Biology;L1CAM interactions;Axon guidance
(Consensus)
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- loftool
- 0.0699
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- 0.206
- hipred
- Y
- hipred_score
- 0.628
- ghis
- 0.591
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lypla2
- Phenotype
Gene ontology
- Biological process
- protein depalmitoylation;fatty acid metabolic process;axon guidance
- Cellular component
- cytoplasm;Golgi stack;cytosol;extracellular exosome
- Molecular function
- palmitoyl-(protein) hydrolase activity;cadherin binding;carboxylic ester hydrolase activity