GPLD1
glycosylphosphatidylinositol specific phospholipase D1
Basic information
Region (hg38): 6:24424565-24495205
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (117 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPLD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001503.4. 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 | 1 | |||||
| missense | 111 | 117 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 111 | 7 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GPLD1 | protein_coding | protein_coding | ENST00000230036 | 25 | 70641 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.59e-15 | 0.980 | 124426 | 8 | 1314 | 125748 | 0.00527 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.296 | 505 | 487 | 1.04 | 0.0000272 | 5455 |
| Missense in Polyphen | 178 | 174.36 | 1.0209 | 1949 | ||
| Synonymous | 0.104 | 198 | 200 | 0.991 | 0.0000132 | 1651 |
| Loss of Function | 2.53 | 32 | 51.6 | 0.620 | 0.00000270 | 583 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00327 | 0.00327 |
| Ashkenazi Jewish | 0.00357 | 0.00358 |
| East Asian | 0.000598 | 0.000598 |
| Finnish | 0.0217 | 0.0216 |
| European (Non-Finnish) | 0.00579 | 0.00577 |
| Middle Eastern | 0.000598 | 0.000598 |
| South Asian | 0.00152 | 0.00150 |
| Other | 0.00410 | 0.00392 |
dbNSFP
Source:
- Function
- FUNCTION: This protein hydrolyzes the inositol phosphate linkage in proteins anchored by phosphatidylinositol glycans (GPI-anchor) thus releasing these proteins from the membrane.;
- Pathway
- Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Homo sapiens (human);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins;adp-ribosylation factor;Phosphatidylinositol phosphate metabolism;Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.962
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 70.78
Haploinsufficiency Scores
- pHI
- 0.295
- hipred
- N
- hipred_score
- 0.431
- ghis
- 0.517
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.633
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gpld1
- Phenotype
- endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- ossification;cell migration involved in sprouting angiogenesis;chondrocyte differentiation;complement receptor mediated signaling pathway;C-terminal protein lipidation;GPI anchor release;negative regulation of cell population proliferation;insulin receptor signaling pathway;response to glucose;positive regulation of endothelial cell migration;positive regulation of alkaline phosphatase activity;positive regulation of triglyceride biosynthetic process;negative regulation of triglyceride catabolic process;positive regulation of glucose metabolic process;positive regulation of high-density lipoprotein particle clearance;cellular response to insulin stimulus;cellular response to drug;hematopoietic stem cell migration;positive regulation of insulin secretion involved in cellular response to glucose stimulus;positive regulation of apoptotic process;positive regulation of cytolysis;phosphatidylcholine metabolic process;positive regulation of membrane protein ectodomain proteolysis;positive regulation of secretion;transepithelial transport;cellular response to calcium ion;cellular response to cholesterol;cellular response to triglyceride;cellular response to pH;hematopoietic stem cell migration to bone marrow;regulation of cellular response to insulin stimulus
- Cellular component
- extracellular region;extracellular space;cytoplasm;lysosomal membrane;extracellular matrix;intracellular membrane-bounded organelle;extracellular exosome
- Molecular function
- glycosylphosphatidylinositol phospholipase D activity;phospholipase D activity;sodium channel regulator activity