PGAP3

Protein identityUniProt · HPA

UniProt accession

Q96FM1

Gene

PGAP3

Ensembl

ENSG00000161395

Chromosome

17

Canonical length

320 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins, Predicted membrane proteins

Subcellular location

Plasma membrane,Cytosol

OverviewNCBI Gene

This gene encodes a glycosylphosphatidylinositol (GPI)-specific phospholipase that primarily localizes to the Golgi apparatus. This ubiquitously expressed gene is predicted to encode a seven-transmembrane protein that removes unsaturated fatty acids from the sn-2 position of GPI. The remodeling of the constituent fatty acids on GPI is thought to be important for the proper association between GPI-anchored proteins and lipid rafts. The tethering of proteins to plasma membranes via posttranslational GPI-anchoring is thought to play a role in protein sorting and trafficking. Mutations in this gene cause an autosomal recessive form of neurologic hyperphosphatasia with cognitive disability (HPMRS4). Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]

Canonical amino-acid sequenceUniProt

320 residues, UniProt reviewed canonical sequence.

>Q96FM1|PGAP3
     1  MAGLAARLVL LAGAAALASG SQGDREPVYR DCVLQCEEQN CSGGALNHFR SRQPIYMSLA
    61  GWTCRDDCKY ECMWVTVGLY LQEGHKVPQF HGKWPFSRFL FFQEPASAVA SFLNGLASLV
   121  MLCRYRTFVP ASSPMYHTCV AFAWVSLNAW FWSTVFHTRD TDLTEKMDYF CASTVILHSI
   181  YLCCVRTVGL QHPAVVSAFR ALLLLMLTVH VSYLSLIRFD YGYNLVANVA IGLVNVVWWL
   241  AWCLWNQRRL PHVRKCVVVV LLLQGLSLLE LLDFPPLFWV LDAHAIWHIS TIPVHVLFFS
   301  FLEDDSLYLL KESEDKFKLD

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PGAP3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Other membrane

Secreted

No

Transmembrane segments

7

Mean surface accessibility (rSASA)

0.29

Highest tissue expression

35 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PGAP3.

Disease | AllUniProt

Conditions PGAP3 is implicated in, by any mechanism.

• Hyperphosphatasia with impaired intellectual development syndrome 4 (HPMRS4) MIM:615716

Disease | GeneticClinVar

40 pathogenic / likely-pathogenic of 249 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Hyperphosphatasia with intellectual disability syndrome 4
• Inborn genetic diseases
• PGAP3-related disorder
• Hyperphosphatasia-intellectual disability syndrome

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

0.83

gnomAD pLI

0

gnomAD missense Z

0.69

DepMap mean gene effect

-0.15

DepMap dependency class

selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• GPI anchor biosynthetic process
• GPI anchor metabolic process

Molecular functions

• acting on ester bonds
• hydrolase activity

Cellular components

• cytoplasmic vesicle
• endoplasmic reticulum membrane
• Golgi membrane

Protein domainsUniProt · Pfam · InterPro

• Per1-like
• Per1-like family

KeywordsUniProt

• Glycoprotein
• Golgi apparatus
• GPI-anchor biosynthesis
• Hydrolase
• Intellectual disability
• Membrane
• Signal
• Transmembrane
• Transmembrane helix