PGAP3
Basic information
Region (hg38): 17:39671122-39696797
Previous symbols: [ "PERLD1" ]
Links
Phenotypes
GenCC
Source:
- hyperphosphatasia with intellectual disability syndrome 4 (Definitive), mode of inheritance: AR
- hyperphosphatasia with intellectual disability syndrome 4 (Strong), mode of inheritance: AR
- hyperphosphatasia-intellectual disability syndrome (Supportive), mode of inheritance: AR
- hyperphosphatasia with intellectual disability syndrome 4 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Hyperphosphatasia with impaired intellectual development syndrome 4 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 22315194; 24439110; 29620724; 30217754; 30345601 |
ClinVar
This is a list of variants' phenotypes submitted to
- Hyperphosphatasia with intellectual disability syndrome 4 (9 variants)
- not provided (5 variants)
- Inborn genetic diseases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGAP3 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 | 40 | 43 | ||||
missense | 57 | 71 | ||||
nonsense | 7 | |||||
start loss | 0 | |||||
frameshift | 7 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 1 | 4 | 5 | |||
non coding | 18 | 14 | 35 | |||
Total | 12 | 11 | 60 | 66 | 16 |
Highest pathogenic variant AF is 0.0000197
Variants in PGAP3
This is a list of pathogenic ClinVar variants found in the PGAP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-39672243-T-C | Benign (Jan 22, 2024) | |||
17-39672243-TG-CA | Uncertain significance (Oct 23, 2022) | |||
17-39672244-G-A | Hyperphosphatasia with intellectual disability syndrome 4 | Uncertain significance (Aug 26, 2021) | ||
17-39672492-A-G | Benign (Jul 27, 2018) | |||
17-39672534-G-A | Benign (Jul 27, 2018) | |||
17-39672828-G-A | Inborn genetic diseases | Uncertain significance (Aug 08, 2022) | ||
17-39672845-C-T | Likely benign (Nov 08, 2023) | |||
17-39672847-G-C | Uncertain significance (Jun 11, 2022) | |||
17-39672852-T-C | Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic/Likely pathogenic (Oct 23, 2023) | ||
17-39672876-A-G | Hyperphosphatasia with intellectual disability syndrome 4 | Benign (Feb 01, 2024) | ||
17-39672884-A-G | Benign (Jan 25, 2024) | |||
17-39672885-G-C | Likely benign (Oct 13, 2023) | |||
17-39673053-G-GA | Hyperphosphatasia with intellectual disability syndrome 4 | Likely pathogenic (Mar 16, 2022) | ||
17-39673089-C-A | Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic (Mar 01, 2016) | ||
17-39673094-T-C | Hyperphosphatasia with intellectual disability syndrome 4 | Uncertain significance (Jan 09, 2022) | ||
17-39673099-T-C | 10 conditions • Hyperphosphatasia with intellectual disability syndrome 4 • See cases | Pathogenic/Likely pathogenic (Dec 03, 2024) | ||
17-39673100-G-A | Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic/Likely pathogenic (Mar 17, 2024) | ||
17-39673100-G-C | Hyperphosphatasia with intellectual disability syndrome 4 | Conflicting classifications of pathogenicity (Sep 01, 2022) | ||
17-39673105-T-C | Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic (Oct 04, 2016) | ||
17-39673108-A-G | Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic (Mar 01, 2016) | ||
17-39673111-A-G | Inborn genetic diseases | Uncertain significance (Mar 18, 2024) | ||
17-39673122-C-T | Likely benign (Oct 04, 2023) | |||
17-39673123-G-A | Inborn genetic diseases • PGAP3-related disorder • Hyperphosphatasia with intellectual disability syndrome 4 | Pathogenic/Likely pathogenic (Mar 20, 2024) | ||
17-39673128-G-A | Likely benign (Nov 22, 2022) | |||
17-39673131-G-T | Inborn genetic diseases | Uncertain significance (Aug 10, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PGAP3 | protein_coding | protein_coding | ENST00000300658 | 8 | 25676 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00194 | 0.978 | 125736 | 0 | 12 | 125748 | 0.0000477 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.685 | 154 | 180 | 0.856 | 0.0000109 | 2019 |
Missense in Polyphen | 53 | 59.847 | 0.88559 | 748 | ||
Synonymous | 0.671 | 73 | 80.7 | 0.905 | 0.00000514 | 650 |
Loss of Function | 2.05 | 7 | 15.8 | 0.444 | 6.77e-7 | 167 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000455 | 0.0000439 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the lipid remodeling steps of GPI-anchor maturation. Lipid remodeling steps consist in the generation of 2 saturated fatty chains at the sn-2 position of GPI-anchors proteins. Required for phospholipase A2 activity that removes an acyl-chain at the sn-2 position of GPI-anchors during the remodeling of GPI (Probable). {ECO:0000305|PubMed:17021251}.;
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- loftool
- 0.177
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.41
Haploinsufficiency Scores
- pHI
- 0.325
- hipred
- N
- hipred_score
- 0.369
- ghis
- 0.479
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.339
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pgap3
- Phenotype
- limbs/digits/tail phenotype; immune system phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype;
Gene ontology
- Biological process
- GPI anchor metabolic process;GPI anchor biosynthetic process
- Cellular component
- Golgi membrane;integral component of membrane;intrinsic component of endoplasmic reticulum membrane
- Molecular function
- hydrolase activity, acting on ester bonds