PGAP3

post-GPI attachment to proteins phospholipase 3

Basic information

Region (hg38): 17:39671122-39696797

Previous symbols: [ "PERLD1" ]

Links

ENSG00000161395

∙ NCBI:93210 ∙ OMIM:611801 ∙ HGNC:23719 ∙ Uniprot:Q96FM1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

hyperphosphatasia with intellectual disability syndrome 4 (Definitive), mode of inheritance: AR
hyperphosphatasia-intellectual disability syndrome (Supportive), mode of inheritance: AR
hyperphosphatasia with intellectual disability syndrome 4 (Strong), mode of inheritance: AR
hyperphosphatasia with intellectual disability syndrome 4 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the PGAP3 gene.

not_provided (144 variants)
Inborn_genetic_diseases (50 variants)
Hyperphosphatasia_with_intellectual_disability_syndrome_4 (38 variants)
PGAP3-related_disorder (8 variants)
not_specified (2 variants)
Hyperphosphatasia-intellectual_disability_syndrome (1 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. These statistics are base on transcript: NM_000033419.5. 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 clinvar	49 clinvar	2 clinvar	52
missense	8 clinvar	8 clinvar	75 clinvar	11 clinvar	1 clinvar	103
nonsense	8 clinvar	3 clinvar				11
start loss						0
frameshift	8 clinvar	4 clinvar				12
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar				4
Total	26	17	76	60	3

Highest pathogenic variant AF is 0.00040988

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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