Seroatlas · Human Serome Atlas

PGAP4

GPI-N-acetylgalactosamine transferase PGAP4

Also known as: C9orf125, MGC12992, PGAP4_HUMAN, TMEM246

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9BRR3
Gene: PGAP4
Ensembl: ENSG00000165152
Chromosome: 9
Canonical length: 403 aa
Protein class: Predicted membrane proteins
Subcellular location: Endoplasmic reticulum,Vesicles

OverviewNCBI Gene

Enables glycosyltransferase activity. Involved in GPI anchor biosynthetic process. Located in Golgi membrane. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

403 residues, UniProt reviewed canonical sequence.

>Q9BRR3|PGAP4
     1  MSTSTSPAAM LLRRLRRLSW GSTAVQLFIL TVVTFGLLAP LACHRLLHSY FYLRHWHLNQ
    61  MSQEFLQQSL KEGEAALHYF EELPSANGSV PIVWQATPRP WLVITIITVD RQPGFHYVLQ
   121  VVSQFHRLLQ QCGPQCEGHQ LFLCNVERSV SHFDAKLLSK YVPVANRYEG TEDDYGDDPS
   181  TNSFEKEKQD YVYCLESSLQ TYNPDYVLMV EDDAVPEEQI FPVLEHLLRA RFSEPHLRDA
   241  LYLKLYHPER LQHYINPEPM RILEWVGVGM LLGPLLTWIY MRFASRPGFS WPVMLFFSLY
   301  SMGLVELVGR HYFLELRRLS PSLYSVVPAS QCCTPAMLFP APAARRTLTY LSQVYCHKGF
   361  GKDMALYSLL RAKGERAYVV EPNLVKHIGL FSSLRYNFHP SLL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PGAP4 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: 3
Mean surface accessibility (rSASA): 0.28
Highest tissue expression: 29 nTPM

Expression across tissuesHPA

Tissue

heart muscle: 29 nTPM
cerebellum: 28 nTPM
cerebral cortex: 27 nTPM
hypothalamus: 24 nTPM
hippocampal formation: 17 nTPM
cervix: 16 nTPM

Single-cell type

esophageal apical cells: 61 nCPM
tuft cells: 58 nCPM
esophageal suprabasal cells: 51 nCPM
foveolar cells: 48 nCPM
other brain neurons: 47 nCPM
corticotrophs: 45 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

pons: 67 nTPM
hypothalamus: 67 nTPM
cerebral cortex: 66 nTPM
basal ganglia: 56 nTPM
hippocampal formation: 54 nTPM
white matter: 53 nTPM

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): 0.7
gnomAD pLI: 0.09
DepMap mean gene effect: 0.08
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Protein domainsUniProt · Pfam · InterPro

GPI-GalNAc transferase PGAP4

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads PGAP4 as an antibody target. Whether an autoantibody or antibody against PGAP4 could matter depends on whether native PGAP4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PGAP4 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label PGAP4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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