GDPD1
Basic information
Region (hg38): 17:59220467-59275970
Links
Phenotypes
GenCC
Source:
- retinitis pigmentosa (Limited), mode of inheritance: AD
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 GDPD1 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 GDPD1
This is a list of pathogenic ClinVar variants found in the GDPD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-59220712-A-C | not specified | Uncertain significance (Nov 01, 2022) | ||
| 17-59234531-A-G | not specified | Uncertain significance (Dec 07, 2024) | ||
| 17-59245427-G-A | not specified | Uncertain significance (Aug 09, 2021) | ||
| 17-59245514-G-A | not specified | Uncertain significance (Dec 06, 2024) | ||
| 17-59245538-C-A | not specified | Uncertain significance (Nov 18, 2022) | ||
| 17-59257166-G-C | not specified | Uncertain significance (May 11, 2022) | ||
| 17-59257811-T-G | not specified | Uncertain significance (Jan 22, 2025) | ||
| 17-59267074-C-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 17-59267122-G-C | not specified | Uncertain significance (Jan 18, 2025) | ||
| 17-59267164-A-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 17-59270979-A-C | not specified | Uncertain significance (Jan 26, 2023) | ||
| 17-59270985-C-T | not specified | Uncertain significance (Jul 11, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GDPD1 | protein_coding | protein_coding | ENST00000284116 | 10 | 55501 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00262 | 0.995 | 125720 | 0 | 25 | 125745 | 0.0000994 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.56 | 106 | 162 | 0.654 | 0.00000777 | 2045 |
| Missense in Polyphen | 28 | 60.696 | 0.46132 | 754 | ||
| Synonymous | 0.0215 | 60 | 60.2 | 0.996 | 0.00000283 | 589 |
| Loss of Function | 2.62 | 8 | 20.9 | 0.382 | 0.00000117 | 238 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000522 | 0.000521 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000125 | 0.000123 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000668 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine. {ECO:0000250|UniProtKB:Q9CRY7}.;
- Pathway
- Ether lipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Glycerophospholipid catabolism;PI Metabolism;Phospholipid metabolism
(Consensus)
Intolerance Scores
- loftool
- 0.546
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.288
- hipred
- Y
- hipred_score
- 0.554
- ghis
- 0.642
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gdpd1
- Phenotype
Gene ontology
- Biological process
- phospholipid metabolic process;glycerophospholipid catabolic process;N-acylethanolamine metabolic process
- Cellular component
- endoplasmic reticulum membrane;membrane;integral component of membrane;perinuclear region of cytoplasm
- Molecular function
- lysophospholipase activity;phosphoric diester hydrolase activity;metal ion binding;alkylglycerophosphoethanolamine phosphodiesterase activity