LYPLA2
Basic information
Region (hg38): 1:23791110-23795539
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (21 variants)
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. These statistics are base on transcript: NM_000007260.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 21 | 21 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 0 | 0 |
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