Seroatlas · Human Serome Atlas

POMGNT1

Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1

Also known as: FLJ20277, LGMD2O, MEB, MGAT1.2, PMGT1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q8WZA1
Gene: POMGNT1
Ensembl: ENSG00000085998
Chromosome: 1
Canonical length: 660 aa
Protein class: Disease related genes, Human disease related genes, Metabolic proteins, Predicted membrane proteins

OverviewNCBI Gene

This gene encodes a type II transmembrane protein that resides in the Golgi apparatus. It participates in O-mannosyl glycosylation and is specific for alpha linked terminal mannose. Mutations in this gene may be associated with muscle-eye-brain disease and several congenital muscular dystrophies. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

Canonical amino-acid sequenceUniProt

660 residues, UniProt reviewed canonical sequence.

>Q8WZA1|POMGNT1
     1  MDDWKPSPLI KPFGARKKRS WYLTWKYKLT NQRALRRFCQ TGAVLFLLVT VIVNIKLILD
    61  TRRAISEANE DPEPEQDYDE ALGRLEPPRR RGSGPRRVLD VEVYSSRSKV YVAVDGTTVL
   121  EDEAREQGRG IHVIVLNQAT GHVMAKRVFD TYSPHEDEAM VLFLNMVAPG RVLICTVKDE
   181  GSFHLKDTAK ALLRSLGSQA GPALGWRDTW AFVGRKGGPV FGEKHSKSPA LSSWGDPVLL
   241  KTDVPLSSAE EAECHWADTE LNRRRRRFCS KVEGYGSVCS CKDPTPIEFS PDPLPDNKVL
   301  NVPVAVIAGN RPNYLYRMLR SLLSAQGVSP QMITVFIDGY YEEPMDVVAL FGLRGIQHTP
   361  ISIKNARVSQ HYKASLTATF NLFPEAKFAV VLEEDLDIAV DFFSFLSQSI HLLEEDDSLY
   421  CISAWNDQGY EHTAEDPALL YRVETMPGLG WVLRRSLYKE ELEPKWPTPE KLWDWDMWMR
   481  MPEQRRGREC IIPDVSRSYH FGIVGLNMNG YFHEAYFKKH KFNTVPGVQL RNVDSLKKEA
   541  YEVEVHRLLS EAEVLDHSKN PCEDSFLPDT EGHTYVAFIR MEKDDDFTTW TQLAKCLHIW
   601  DLDVRGNHRG LWRLFRKKNH FLMVGVPASP YSVKKPPSVT PIFLEPPPKE EGAPGAPEQT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against POMGNT1 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: 1
Mean surface accessibility (rSASA): 0.3
Highest tissue expression: 79 nTPM

Expression across tissuesHPA

Tissue

parathyroid gland: 79 nTPM
heart muscle: 68 nTPM
spinal cord: 52 nTPM
skeletal muscle: 52 nTPM
tongue: 42 nTPM
thyroid gland: 31 nTPM

Single-cell type

endometrial luminal cells: 259 nCPM
cardiomyocytes: 142 nCPM
endometrial glandular cells: 80 nCPM
epididymal clear cells: 53 nCPM
oligodendrocytes: 47 nCPM
prostatic glandular cells: 41 nCPM

Immune cell

NK-cell: 5.8 nTPM
plasmacytoid DC: 3.6 nTPM
naive CD4 T-cell: 3.5 nTPM
gdT-cell: 2.8 nTPM
naive CD8 T-cell: 2.7 nTPM
memory CD8 T-cell: 2.4 nTPM

Brain region

white matter: 54 nTPM
medulla oblongata: 47 nTPM
midbrain: 43 nTPM
cerebellum: 41 nTPM
spinal cord: 40 nTPM
thalamus: 39 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about POMGNT1.

Disease | AllUniProt

Conditions POMGNT1 is implicated in, by any mechanism.

Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A3 (MDDGA3) MIM:253280
Muscular dystrophy-dystroglycanopathy congenital with impaired intellectual development B3 (MDDGB3) MIM:613151
Muscular dystrophy-dystroglycanopathy limb-girdle C3 (MDDGC3) MIM:613157
Retinitis pigmentosa 76 (RP76) MIM:617123

Disease | GeneticClinVar

261 pathogenic / likely-pathogenic of 1,549 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3
Autosomal recessive limb-girdle muscular dystrophy type 2O
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A3
Muscle eye brain disease
Retinitis pigmentosa 76

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): 1.04
gnomAD pLI: 0
gnomAD missense Z: 0.9
DepMap mean gene effect: -0.08
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

Glycosyl transferase, family 13
Nucleotide-diphospho-sugar transferases
ILEI/PANDER domain
GNT-I family
Interleukin-like EMT inducer
Protein O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1, PANDER-like domain
O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of POMGNT1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads POMGNT1 as an antibody target. Whether an autoantibody or antibody against POMGNT1 could matter depends on whether native POMGNT1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

POMGNT1 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 POMGNT1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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