GNPTAB

gene
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Also known as KIAA1208MGC4170

Summary

GNPTAB (N-acetylglucosamine-1-phosphate transferase subunits alpha and beta, HGNC:29670) is a protein-coding gene on chromosome 12q23.2, encoding N-acetylglucosamine-1-phosphotransferase subunits alpha/beta (Q3T906). Catalyzes the formation of mannose 6-phosphate (M6P) markers on high mannose type oligosaccharides in the Golgi apparatus.

This gene encodes two of three subunit types of the membrane-bound enzyme N-acetylglucosamine-1-phosphotransferase, a heterohexameric complex composed of two alpha, two beta, and two gamma subunits. The encoded protein is proteolytically cleaved at the Lys928-Asp929 bond to yield mature alpha and beta polypeptides while the gamma subunits are the product of a distinct gene (GeneID 84572). In the Golgi apparatus, the heterohexameric complex catalyzes the first step in the synthesis of mannose 6-phosphate recognition markers on certain oligosaccharides of newly synthesized lysosomal enzymes. These recognition markers are essential for appropriate trafficking of lysosomal enzymes. Mutations in this gene have been associated with both mucolipidosis II and mucolipidosis IIIA.

Source: NCBI Gene 79158 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): GNPTAB-mucolipidosis (Definitive, ClinGen) — +3 more curated relationships
  • GWAS associations: 2
  • Clinical variants (ClinVar): 1,790 total — 209 pathogenic, 187 likely-pathogenic
  • Phenotypes (HPO): 192
  • MANE Select transcript: NM_024312

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29670
Approved symbolGNPTAB
NameN-acetylglucosamine-1-phosphate transferase subunits alpha and beta
Location12q23.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1208, MGC4170
Ensembl geneENSG00000111670
Ensembl biotypeprotein_coding
OMIM607840
Entrez79158

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 11 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000299314, ENST00000392919, ENST00000549165, ENST00000549194, ENST00000549738, ENST00000549940, ENST00000550352, ENST00000550718, ENST00000552009, ENST00000552681, ENST00000647144, ENST00000917133, ENST00000917134, ENST00000917135, ENST00000917136, ENST00000953730

RefSeq mRNA: 1 — MANE Select: NM_024312 NM_024312

CCDS: CCDS9088

Canonical transcript exons

ENST00000299314 — 21 exons

ExonStartEnd
ENSE00001101296101770996101771157
ENSE00001101359101786012101786217
ENSE00001155408101780152101780286
ENSE00001155415101780557101780621
ENSE00001155433101789938101790057
ENSE00001265267101745499101747241
ENSE00001265274101749101101749191
ENSE00001265287101757212101757310
ENSE00001265305101761127101761346
ENSE00001265345101796677101796762
ENSE00001265380101760030101760143
ENSE00001265394101761564101761763
ENSE00001265404101766091101766294
ENSE00001265409101768037101768160
ENSE00001265416101770021101770191
ENSE00001265452101764202101765304
ENSE00001319970101770406101770585
ENSE00002380951101830559101830959
ENSE00003587415101788548101788589
ENSE00003594751101753372101753539
ENSE00003653576101757572101757657

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 97.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.7076 / max 543.1891, expressed in 1789 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
13291116.78461748
1329124.15811469
1329100.2583115
1329090.220776
1329130.174670
2068630.111344

Top tissues by expression

292 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097997.32gold quality
endothelial cellCL:000011597.00gold quality
sural nerveUBERON:001548896.86gold quality
cortical plateUBERON:000534396.68gold quality
parotid glandUBERON:000183195.45gold quality
urethraUBERON:000005795.35gold quality
skin of hipUBERON:000155494.83gold quality
epithelium of nasopharynxUBERON:000195194.57gold quality
nasopharynxUBERON:000172894.55gold quality
upper leg skinUBERON:000426294.34gold quality
saliva-secreting glandUBERON:000104494.22gold quality
minor salivary glandUBERON:000183093.86gold quality
rectumUBERON:000105293.76gold quality
colonic mucosaUBERON:000031793.71gold quality
palpebral conjunctivaUBERON:000181293.63gold quality
mucosa of sigmoid colonUBERON:000499393.60gold quality
caudate nucleusUBERON:000187393.45gold quality
nucleus accumbensUBERON:000188293.39gold quality
mouth mucosaUBERON:000372993.39gold quality
anterior cingulate cortexUBERON:000983593.20gold quality
superficial temporal arteryUBERON:000161493.17gold quality
cingulate cortexUBERON:000302793.14gold quality
visceral pleuraUBERON:000240193.12gold quality
amygdalaUBERON:000187693.10gold quality
lower lobe of lungUBERON:000894993.10gold quality
CA1 field of hippocampusUBERON:000388192.97gold quality
mucosa of paranasal sinusUBERON:000503092.96gold quality
dorsolateral prefrontal cortexUBERON:000983492.79gold quality
putamenUBERON:000187492.68gold quality
renal glomerulusUBERON:000007492.64gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-6701yes91.56
E-CURD-122yes44.15
E-MTAB-6678yes31.65
E-GEOD-125970yes22.93
E-CURD-112yes15.30
E-ANND-3yes15.22
E-GEOD-135922yes7.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

103 targeting GNPTAB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-8485100.0077.574731
HSA-MIR-5692A100.0074.406850
HSA-MIR-3646100.0073.565283
HSA-MIR-450099.9972.722367
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-366299.9973.825684
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-493-5P99.9672.472382
HSA-LET-7C-3P99.9573.422862
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-1-3P99.9372.351914
HSA-MIR-20699.9372.501893
HSA-MIR-61399.9171.501710
HSA-MIR-3529-3P99.9073.553045
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-4697-3P99.8967.091123

Literature-anchored findings (GeneRIF, showing 40)

  • GNPTAB alpha and beta subunits are encoded by a single cDNA (PMID:16120602)
  • results provide evidence that GNPTA encodes a subunit of GlcNAc-1-phosphotransferase defective in individuals with mucolipidosis II (PMID:16200072)
  • 15 different mutations in GNPTAB from 18 pedigrees with Mucolipidosis II or mucolipidosis IIIA were found. (PMID:16465621)
  • The results of this study confirm that Mucolipidosis (ML) II or ML III phenotype is not due to the localization of the mutations, but rather to the severity of the GNPTA mutations (PMID:16630736)
  • A single mutation (c.3503_3504delTC) is the allele causing Mucolipidosis II in the Saguenay-Lac-Saint-Jean population, and its high carrier rate is most likely explained by a founder effect. (PMID:18190596)
  • The GNPTAB gene was analyzed in 25 Mucolipidosis II and 15 ML III Japanese patients. (PMID:19197337)
  • Fifty-one pathogenic changes in GNPTAB are presented, including 42 novel mutations causing mucolipidoses II and III alpha/beta. (PMID:19617216)
  • Mutations within the GNPTAB gene are associated with Mucolipidoses. (PMID:19634183)
  • The study led to the identification of 11 different mutations in GNPTAB and GNPTG genes in 13 mucolipidosis II and III patients. (PMID:19659762)
  • identified 3 mutations in GNPTAB gene in subjects with stuttering (PMID:20147709)
  • proteolytic processing of the gamma-subunit represents a novel mechanism to regulate GlcNAc-1-phosphotransferase activity and the subsequent sorting of lysosomal enzymes (PMID:20489197)
  • Patients carrying the c.3503_3504delTC deletion in the N-acetylglucosamine-1-phosphotransferase gene are presented with a common haplotype, which implies a common origin of this mutation in the Mediterranian Region. (PMID:20880125)
  • Glu1200Lys mutation in GNPTAB gene is founder mutation associated with persistent stuttering (PMID:20944643)
  • By using linkage and mutational analyses, there have identified that the family members contain compound heterozygous mutations of p.R364X and c.2715+1G>A in the GNPTAB gene. (PMID:21549105)
  • To date mutations in GNPTAB, GNPTG, and NAGPA have been associated with stuttering. These genes encode the lysosomal enzyme targeting pathway, defective in mucolipidosis. (Review) (PMID:22884963)
  • data suggest that the oligomeric type III membrane protein PT complex requires a combinatorial sorting motif that forms a tertiary epitope to be recognized by distinct sites within the coat protein complex II machinery (PMID:23192343)
  • The mutation c.2808A>G creates a new splice site in exon 14 of GNPATB gene. (PMID:23566849)
  • The DMAP interaction domain of the alpha subunit functions in the selective recognition of acid hydrolase substrates and provides an explanation for the impaired phosphorylation of acid hydrolases in a patient with mucolipidosis II. (PMID:23733939)
  • study located two homozygous nonsense mutations in the GNPTAB gene, c.1071G>A (p.W357X) and c.1090C>T (p.R364X) in two patients with mucolipidosis II alpha/beta (PMID:23773965)
  • A novel intermediate mucolipidosis II/IIIalphabeta caused by GNPTAB mutation in the cytosolic N-terminal domain. (PMID:24045841)
  • both missense and frameshift mutations are associated with a severe clinical phenotype causing retention of the protein in the endoplasmic reticulum and failure to cleave the alpha/beta-subunit precursor protein are associated with a severe clinical phenotype (PMID:24375680)
  • Missense mutations impair retention of the catalytically active enzyme in the Golgi complex resulting in mistargeting of the mutant phosphotransferases to lysosomes, where they are degraded, or to the cell surface and release into the medium. (PMID:24550498)
  • novel mouse model of MLII homozygous for a patient mutation in the GNPTAB gene. (PMID:25107912)
  • SNPs covering GNPTAB, GNPTG and NAGPA were subjected to genotyping, association analysis was performed on all SNPs. Significant association of rs17031962 in GNPTAB and rs882294 in NAGPA with developmental dyslexia in a Chinese population was identified after false discovery rate correction for multiple comparisons. (PMID:25643770)
  • Persistent stuttering is associated with mutations in GNPTAB that are generally not found in mucolipidosis . (PMID:26130485)
  • GlcNAc-1-phosphotransferase gamma-subunits bind to glycosylated region in the no-similarity domain 2 of alpha-subunit, which is independent on cysteine 70 identified to be responsible for alpha-subunit homodimerization. (PMID:26385638)
  • we described five individuals from a large consanguineous Turkish family with MLIIIalpha/beta and identified a novel homozygous missense genetic variant in the alpha subunit of GNPTAB gene in five patients (PMID:26749367)
  • These findings serve to explain how GlcNAc-1-phosphotransferase recognizes a large number of proteins that lack a common structural motif. (PMID:26833567)
  • GNPTAB mutations are associated with mucolipidosis II. (PMID:27180337)
  • Mutations of the GNPTAB gene is associated with mucolipidosis type III. (PMID:27710913)
  • GNPTAB missense mutations cause loss of GlcNAc-1-phosphotransferase activity in mucolipidosis type II (PMID:28918368)
  • 14 variations were found in GNPTAB, GNPTG and NAGPA genes. (PMID:29289611)
  • The diagnosis of Mucolipidosis II is often missed, as it may present with rickets-like picture. In this article, we describe two neonatal mucolipidosis II patients mimicking rickets, and we evaluated them by clinical, metabolic and imaging findings via literature and also emphasized the difficulties in diagnosis of this rare disease. (PMID:30204966)
  • Study identifies GNPTAB as a host factor for Ebola virus (EBOV) infection. This requirement is confirmed in primary cells from mucolipidosis II and mucolipidosis III patients with defective GNPTAB variants. An inhibitor of the SKI-1/S1P protease required for GNPTAB activity blocks EBOV infection, suggesting that targeting GNPTAB may be a strategy for a host-targeted antiviral therapy for EBOV. (PMID:30655525)
  • Data provide an overview on 258 mutations in GNPTAB including 58 novel ones. Comprehensive functional studies of GNPTAB missense mutations did not only gain insights into the composition and function of the GlcNAc-1-phosphotransferase, but also helped to define genotype-phenotype correlations to predict the clinical outcome in patients with mucolipidosis. (PMID:30882951)
  • We evaluated 51 stuttering individuals with a mutation in either the GNPTAB, GNPTG, NAGPA, or AP4E1 gene. Mutation carriers achieved significantly less resolution in PSI following therapy, with PSI scores showing significantly less improvement in individuals who carry a mutation (p = 0.0157, RR = 1.75, OR = 2.92) while the group difference in DWS between carriers and non-carriers was statistically not significant. (PMID:31003007)
  • These data suggest that vocalization defects in mice carrying human stuttering mutations in Gnptab derive from abnormalities in astrocytes, particularly in the corpus callosum, and provide support for hypotheses that focus on deficits in interhemispheric communication in stuttering. (PMID:31405983)
  • Combined in vitro and in silico analyses of missense mutations in GNPTAB provide new insights into the molecular bases of mucolipidosis II and III alpha/beta. (PMID:31579991)
  • Structures of Bacterial MraY and Human GPT Provide Insights into Rational Antibiotic Design. (PMID:32199982)
  • Disease-causing missense mutations within the N-terminal transmembrane domain of GlcNAc-1-phosphotransferase impair endoplasmic reticulum translocation or Golgi retention. (PMID:32220096)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriognptabENSDARG00000030153
mus_musculusGnptabENSMUSG00000035311
rattus_norvegicusGnptabENSRNOG00000005228
drosophila_melanogasterGnptabFBGN0033392
caenorhabditis_elegansWBGENE00007340
caenorhabditis_elegansWBGENE00014666

Protein

Protein identifiers

N-acetylglucosamine-1-phosphotransferase subunits alpha/betaQ3T906 (reviewed: Q3T906)

Alternative names: GlcNAc-1-phosphotransferase subunits alpha/beta, Stealth protein GNPTAB, UDP-N-acetylglucosamine-1-phosphotransferase subunits alpha/beta

All UniProt accessions (6): Q3T906, F8VQW2, H0YIE6, H0YIK3, H0YIU2, Q9BUA5

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the formation of mannose 6-phosphate (M6P) markers on high mannose type oligosaccharides in the Golgi apparatus. M6P residues are required to bind to the M6P receptors (MPR), which mediate the vesicular transport of lysosomal enzymes to the endosomal/prelysosomal compartment.

Subunit / interactions. Hexamer of two alpha, two beta and two gamma (GNPTG) subunits; disulfide-linked. The alpha and/or the beta subunits of the enzyme constitute the catalytic subunits. Interacts with LYSET; facilitates proper localization of GNPTAB.

Subcellular location. Golgi apparatus membrane Golgi apparatus membrane.

Tissue specificity. Expressed in the heart, whole brain, placenta, lung, liver, skeletal muscle, kidney and pancreas.

Post-translational modifications. The alpha- and beta-subunits are generated by a proteolytic cleavage by MBTPS1 protease at the Lys-928-Asp-929 bond.

Disease relevance. Mucolipidosis type II (MLII) [MIM:252500] Fatal, autosomal recessive, lysosomal storage disorder characterized by severe clinical and radiologic features, peculiar fibroblast inclusions, and no excessive mucopolysacchariduria. Congenital dislocation of the hip, thoracic deformities, hernia, and hyperplastic gums are evident soon after birth. The disease is caused by variants affecting the gene represented in this entry. Mucolipidosis type III complementation group A (MLIIIA) [MIM:252600] Autosomal recessive disease of lysosomal enzyme targeting. Clinically MLIII is characterized by restricted joint mobility, skeletal dysplasia, and short stature. Mildly coarsened facial features and thickening of the skin have been described. Cardiac valvular disease and corneal clouding may also occur. Half of the reported patients show learning disabilities or intellectual disability. The disease is caused by variants affecting the gene represented in this entry. Genetic variations in GNPTAB have been suggested to play a role in susceptibility to persistent stuttering. Stuttering is a common speech disorder characterized by repetitions, prolongations, and interruptions in the flow of speech.

Domain organisation. The DMAP1-binding domain mediates substrate recognition. It specifically recognizes a conformation-dependent protein determinant present in acid hydrolases.

Miscellaneous. Due to the low pH in the endosomal/prelysosomal compartment, the lysosomal enzyme-MPR complex dissociates and then the enzyme is delivered to the lysosome. Between 5% and 20% of newly synthesized lysosomal enzymes escape the binding to the MPR in the Golgi apparatus and are secreted. Stealth proteins are part of a protein family that is conserved from bacteria to higher eukaryotes. Family members were first identified in microbes as proteins that help pathogens to elude the host innate immune system. Microbial stealth proteins are most likely involved in the biosynthesis of exopolysaccharides. Stealth proteins are predicted to function as hexose-1-phosphoryltransferases.

Similarity. Belongs to the stealth family.

Isoforms (2)

UniProt IDNamesCanonical?
Q3T906-11yes
Q3T906-22

RefSeq proteins (1): NP_077288* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000800Notch_domDomain
IPR002048EF_hand_domDomain
IPR010506DMAP1-bdDomain
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR021520Stealth_CR2Domain
IPR031356Stealth_CR4Domain
IPR031357Stealth_CR3Domain
IPR031358Stealth_CR1Domain
IPR035993Notch-like_dom_sfHomologous_superfamily
IPR041536GNPTAB_regDomain
IPR047141StealthFamily

Pfam: PF00066, PF06464, PF11380, PF17101, PF17102, PF17103, PF18440

Enzyme classification (BRENDA):

  • EC 2.7.8.17 — UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase (BRENDA: 11 organisms, 41 substrates, 24 inhibitors, 33 Km, 18 kcat entries)

Substrate kinetics (BRENDA)

12 substrates with measured Km, best-characterized 12. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
METHYL-ALPHA-D-MANNOSIDE0.021–1835
UDP-GLCNAC0.021–0.25
UTEROFERRIN0.022–0.0654
CATHEPSIN D0.018–0.0253
DNASE I0.03–0.062
MAN9GLCNAC1 OLIGOSACCHARIDE3.3–5.72
METHYL ALPHA-D-MANNOPYRANOSIDE33–482
NPC20.352–0.3672
PRO-TRIPEPTIDYL PEPTIDASE0.112
RIBONUCLEASE B0.916–1.2442
RNASE B0.5–0.5562
SOYBEAN AGGLUTININ12

Catalyzed reactions (Rhea), 1 shown:

  • N(4)-[alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(glycan)]-L-asparaginyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = N(4)-[6-(N-acetyl-alpha-D-glucosaminyl-1-phospho)-alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(glycan)]-L-asparaginyl-[protein] + UMP + H(+) (RHEA:13581)

UniProt features (145 total): sequence variant 45, helix 28, strand 25, glycosylation site 11, binding site 10, mutagenesis site 5, turn 4, disulfide bond 4, chain 2, transmembrane region 2, splice variant 2, repeat 2, domain 2, sequence conflict 2, site 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
9BGFELECTRON MICROSCOPY2.9
7S05ELECTRON MICROSCOPY3.1
7S06ELECTRON MICROSCOPY3.3
9BGGELECTRON MICROSCOPY3.4
2N6DSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q3T906-F172.150.24

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 928–929 (cleavage; by mbtps1)

Ligand- & substrate-binding residues (10): 467; 516; 531; 534; 1018; 1020; 1022; 1029; 449; 464

Disulfide bonds (4): 438–461, 452–468, 505–528, 519–535

Glycosylation sites (11): 83, 114, 148, 179, 250, 614, 699, 729, 829, 1009, 1129

Mutagenesis-validated functional residues (5):

PositionPhenotype
346partially cleaved by mbtps1.
357abolishes proteolytic cleavage by mbtps1.
925abolishes proteolytic cleavage by mbtps1.
927abolishes proteolytic cleavage by mbtps1.
928abolishes proteolytic cleavage by mbtps1.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 580 (showing top): GOBP_N_GLYCAN_PROCESSING, GOBP_LYSOSOMAL_TRANSPORT, GOBP_VACUOLE_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOBP_PROTEIN_TARGETING, GOBP_VACUOLAR_TRANSPORT, KEGG_LYSOSOME, GOBP_CARBOHYDRATE_PHOSPHORYLATION, SABATES_COLORECTAL_ADENOMA_SIZE_DN, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_PROTEIN_LOCALIZATION_TO_LYSOSOME, ONKEN_UVEAL_MELANOMA_UP

GO Biological Process (7): lysosome organization (GO:0007040), N-glycan processing to lysosome (GO:0016256), secretion of lysosomal enzymes (GO:0033299), carbohydrate phosphorylation (GO:0046835), protein secretion (GO:0009306), protein transport (GO:0015031), establishment of localization in cell (GO:0051649)

GO Molecular Function (6): UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976), calcium ion binding (GO:0005509), protein binding (GO:0005515), transferase activity (GO:0016740), transferase activity, transferring phosphorus-containing groups (GO:0016772), metal ion binding (GO:0046872)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
lytic vacuole organization1
N-glycan processing1
protein targeting to lysosome1
protein secretion1
carbohydrate metabolic process1
phosphorylation1
protein transport1
secretion by cell1
establishment of protein localization to extracellular region1
protein localization to extracellular region1
transport1
intracellular protein localization1
establishment of protein localization1
establishment of localization1
cellular localization1
phosphotransferase activity, for other substituted phosphate groups1
metal ion binding1
binding1
catalytic activity1
transferase activity1
cation binding1
Golgi apparatus1
bounding membrane of organelle1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1342 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
GNPTABGNPTGQ9UJJ9996
GNPTABNAGPAQ9UK23975
GNPTABPURAQ00577872
GNPTABADKP55263817
GNPTABMDH2P40926797
GNPTABRAD51Q06609699
GNPTABFUCA2Q9BTY2598
GNPTABAP4E1Q9UPM8583
GNPTABMBTPS1Q14703568
GNPTABDMAP1Q9NPF5566
GNPTABNAGLUP54802498
GNPTABMANBAO00462494
GNPTABTGP01266491
GNPTABCNTNAP2Q9UHC6488
GNPTABATP2C2O75185470

IntAct

93 interactions, top by confidence:

ABTypeScore
RETREG3PLSCR1psi-mi:“MI:0914”(association)0.640
GNPTGGNPTABpsi-mi:“MI:0914”(association)0.620
GNPTABGNPTGpsi-mi:“MI:0915”(physical association)0.620
B3GALT2GNPTABpsi-mi:“MI:0915”(physical association)0.620
ZNF250GNPTABpsi-mi:“MI:0915”(physical association)0.560
GNPTABPSMA1psi-mi:“MI:0915”(physical association)0.560
GNPTABFAM90A1psi-mi:“MI:0915”(physical association)0.560
GNPTABAENpsi-mi:“MI:0915”(physical association)0.560
GNPTABSTAMBPL1psi-mi:“MI:0915”(physical association)0.560
PSMA1GNPTABpsi-mi:“MI:0915”(physical association)0.560
STAMBPL1GNPTABpsi-mi:“MI:0915”(physical association)0.560
GNPTABZNF250psi-mi:“MI:0915”(physical association)0.560
AENGNPTABpsi-mi:“MI:0915”(physical association)0.560
PICK1ILVBLpsi-mi:“MI:0914”(association)0.530
IGSF6CETN3psi-mi:“MI:0914”(association)0.530
FAM3BLRP5psi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
B3GALT2LTN1psi-mi:“MI:0914”(association)0.530

BioGRID (83): GNPTAB (Two-hybrid), GNPTAB (Two-hybrid), GNPTAB (Two-hybrid), GNPTAB (Two-hybrid), GNPTAB (Two-hybrid), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), GNPTAB (Affinity Capture-MS)

ESM2 similar proteins: B3H5R0, B5DEL3, E2AX35, E9PVB5, F4J2C8, F4JMI5, O00237, O13682, O61608, P22815, P85831, Q09298, Q0WQD2, Q0WV13, Q10025, Q3T906, Q499E0, Q5RGJ8, Q5TEA3, Q5XV99, Q69ZN6, Q6DW74, Q6DW76, Q701R0, Q76B58, Q8GWT1, Q8GWW4, Q8GZ81, Q8RXE1, Q8RXS6, Q8W4A7, Q93ZX7, Q949Q1, Q96AE7, Q9EPZ8, Q9FH36, Q9FWA4, Q9FZ37, Q9H7T0, Q9LE59

Diamond homologs: O68215, O69851, O69853, P9WGD0, P9WGD1, Q3T906, Q4K0S9, Q50025, Q51151, Q5RGJ8, Q5YQ21, Q69ZN6, Q714U9, Q7U184, Q7X4S1, Q83U59, Q84BK9, Q84CZ9, Q84D00, Q8GPD3, Q8KSB4, Q9EVX1, Q9JWW8, Q9L1I2, Q9L1I4, D0U690, F5HID8, Q4JZ13, Q4K2S1, Q4K2U1, Q5KA65, Q69AA9, Q83YR8, Q848R7, Q84CH1, Q8GP72, Q9RGR0, E6RCE9, Q4K0R3, Q6L5Q5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 94 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
R-HSA-425366515.4×4e-03
SLC-mediated transmembrane transport88.0×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1790 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic209
Likely pathogenic187
Uncertain significance414
Likely benign742
Benign54

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1012255NM_024312.5(GNPTAB):c.2980_2983del (p.Ala994fs)Pathogenic
1071081NM_024312.5(GNPTAB):c.1491del (p.Gly498fs)Pathogenic
1072768NM_024312.5(GNPTAB):c.2657_2660del (p.Asp886fs)Pathogenic
1072782NM_024312.5(GNPTAB):c.2423del (p.Leu808fs)Pathogenic
1072926NM_024312.5(GNPTAB):c.2868_2869del (p.Met957fs)Pathogenic
1072933NM_024312.5(GNPTAB):c.3345del (p.Met1116fs)Pathogenic
1073529NM_024312.5(GNPTAB):c.3300_3301del (p.Lys1100fs)Pathogenic
1074624NM_024312.5(GNPTAB):c.1906del (p.Arg636fs)Pathogenic
1075110NM_024312.5(GNPTAB):c.2737_2738del (p.Gln913fs)Pathogenic
1075885NM_024312.5(GNPTAB):c.178_179del (p.Ile60fs)Pathogenic
1252037NM_024312.5(GNPTAB):c.3653del (p.Thr1218fs)Pathogenic
1323026NM_024312.5(GNPTAB):c.1831del (p.Ile611fs)Pathogenic
1323027NM_024312.5(GNPTAB):c.1567T>C (p.Cys523Arg)Pathogenic
1362626NM_024312.5(GNPTAB):c.269del (p.Leu90fs)Pathogenic
1364183NM_024312.5(GNPTAB):c.3100del (p.Ala1034fs)Pathogenic
1382090NM_024312.5(GNPTAB):c.2675del (p.Leu892fs)Pathogenic
1385807NM_024312.5(GNPTAB):c.2334_2338del (p.Ser778fs)Pathogenic
1388742NM_024312.5(GNPTAB):c.3034C>T (p.Gln1012Ter)Pathogenic
1393484NM_024312.5(GNPTAB):c.29_32dup (p.Thr12fs)Pathogenic
1396985NM_024312.5(GNPTAB):c.1186G>T (p.Glu396Ter)Pathogenic
1399558NM_024312.5(GNPTAB):c.2654_2655del (p.Thr885fs)Pathogenic
1416350NM_024312.5(GNPTAB):c.88_89del (p.Thr30fs)Pathogenic
1424471NM_024312.5(GNPTAB):c.2303_2306del (p.Lys768fs)Pathogenic
1429731NM_024312.5(GNPTAB):c.1936dup (p.Gln646fs)Pathogenic
1431816NM_024312.5(GNPTAB):c.1503_1521dup (p.Gly508delinsCysLeuLeuLeuTer)Pathogenic
1437885NM_024312.5(GNPTAB):c.1122dup (p.Arg375fs)Pathogenic
1445251NM_024312.5(GNPTAB):c.1292T>A (p.Leu431Ter)Pathogenic
1451810NM_024312.5(GNPTAB):c.1499del (p.Asn500fs)Pathogenic
1451897NM_024312.5(GNPTAB):c.2923del (p.Glu975fs)Pathogenic
1452514NM_024312.5(GNPTAB):c.2098dup (p.Ile700fs)Pathogenic

SpliceAI

3445 predictions. Top by Δscore:

VariantEffectΔscore
12:101749187:CCCTC:Cacceptor_gain1.0000
12:101749188:CCTCC:Cacceptor_gain1.0000
12:101750085:T:Adonor_gain1.0000
12:101753375:T:Adonor_gain1.0000
12:101753416:T:Adonor_gain1.0000
12:101753536:CTTC:Cacceptor_gain1.0000
12:101753537:TTC:Tacceptor_gain1.0000
12:101753538:TCC:Tacceptor_loss1.0000
12:101753540:C:CCacceptor_gain1.0000
12:101753540:CTGA:Cacceptor_loss1.0000
12:101753541:T:Gacceptor_loss1.0000
12:101757308:AACC:Aacceptor_loss1.0000
12:101757309:ACC:Aacceptor_loss1.0000
12:101757310:CCT:Cacceptor_loss1.0000
12:101757312:T:Aacceptor_loss1.0000
12:101760023:CACTT:Cdonor_loss1.0000
12:101760024:ACTTA:Adonor_loss1.0000
12:101760025:CTTA:Cdonor_loss1.0000
12:101760026:TTA:Tdonor_loss1.0000
12:101760027:TACC:Tdonor_loss1.0000
12:101760028:A:ACdonor_gain1.0000
12:101760028:A:Cdonor_loss1.0000
12:101760028:AC:Adonor_gain1.0000
12:101760029:C:CGdonor_gain1.0000
12:101760029:CC:Cdonor_gain1.0000
12:101760029:CCA:Cdonor_gain1.0000
12:101760029:CCAG:Cdonor_gain1.0000
12:101760029:CCAGG:Cdonor_gain1.0000
12:101760139:AAATC:Aacceptor_gain1.0000
12:101760140:AATC:Aacceptor_gain1.0000

AlphaMissense

8391 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:101753471:A:GL1168P1.000
12:101753474:A:TV1167D1.000
12:101753521:A:CN1151K1.000
12:101753521:A:TN1151K1.000
12:101753527:G:CC1149W1.000
12:101753529:A:GC1149R1.000
12:101761606:G:TP958H1.000
12:101761675:A:GL935P1.000
12:101766135:C:TC523Y1.000
12:101766164:C:AW513C1.000
12:101766164:C:GW513C1.000
12:101766166:A:GW513R1.000
12:101766166:A:TW513R1.000
12:101768063:C:GC461S1.000
12:101768064:A:GC461R1.000
12:101768064:A:TC461S1.000
12:101768078:C:GC456S1.000
12:101768078:C:TC456Y1.000
12:101768079:A:GC456R1.000
12:101768079:A:TC456S1.000
12:101768107:C:AW446C1.000
12:101768107:C:GW446C1.000
12:101768109:A:GW446R1.000
12:101768109:A:TW446R1.000
12:101768119:G:CC442W1.000
12:101768120:C:GC442S1.000
12:101768121:A:GC442R1.000
12:101768121:A:TC442S1.000
12:101768132:C:GC438S1.000
12:101768133:A:GC438R1.000

dbSNP variants (sampled 300 via entrez): RS1000006366 (12:101822244 T>C), RS1000029167 (12:101783712 A>T), RS1000057659 (12:101752931 C>G), RS1000094294 (12:101796447 C>T), RS1000099987 (12:101789907 C>A,T), RS1000162259 (12:101777281 C>G), RS1000163693 (12:101766741 A>G), RS1000184705 (12:101786841 G>A), RS1000226888 (12:101808267 A>G,T), RS1000263810 (12:101814729 A>C), RS1000277945 (12:101796265 G>T), RS1000359565 (12:101831045 G>A,T), RS1000362926 (12:101745848 A>G), RS1000378632 (12:101801967 G>A), RS1000387845 (12:101825325 C>G)

Disease associations

OMIM: gene MIM:607840 | disease phenotypes: MIM:252500, MIM:252600, MIM:252900, MIM:150600, MIM:181440

GenCC curated gene-disease

DiseaseClassificationInheritance
mucolipidosis type IIDefinitiveAutosomal recessive
mucolipidosis type III, alpha/betaDefinitiveAutosomal recessive
mucolipidosisDefinitiveAutosomal recessive
GNPTAB-mucolipidosisStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
GNPTAB-mucolipidosisDefinitiveAR

Mondo (7): mucolipidosis type II (MONDO:0009650), mucolipidosis type III, alpha/beta (MONDO:0018931), mucolipidosis (MONDO:0019248), GNPTAB-mucolipidosis (MONDO:0100122), mucopolysaccharidosis type 3A (MONDO:0009655), Legg-Calve-Perthes disease (MONDO:0007885), Scheuermann disease (MONDO:0008410)

Orphanet (8): Mucolipidosis type III alpha/beta (Orphanet:423461), Mucolipidosis type II (Orphanet:576), Mucolipidosis type III (Orphanet:577), Mucolipidosis (Orphanet:79212), Mucopolysaccharidosis type 3 (Orphanet:581), Sanfilippo syndrome type A (Orphanet:79269), Legg-Calvé-Perthes disease (Orphanet:2380), NON RARE IN EUROPE: Scheuermann’s disease (Orphanet:3135)

HPO phenotypes

192 total (30 of 192 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000023Inguinal hernia
HP:0000105Enlarged kidney
HP:0000154Wide mouth
HP:0000158Macroglossia
HP:0000212Gingival overgrowth
HP:0000243Trigonocephaly
HP:0000252Microcephaly
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000293Full cheeks
HP:0000303Mandibular prognathia
HP:0000316Hypertelorism
HP:0000341Narrow forehead
HP:0000343Long philtrum
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000369Low-set ears
HP:0000388Otitis media
HP:0000403Recurrent otitis media
HP:0000405Conductive hearing impairment
HP:0000407Sensorineural hearing impairment
HP:0000463Anteverted nares
HP:0000470Short neck
HP:0000484Hyperopic astigmatism
HP:0000485Megalocornea
HP:0000488Retinopathy
HP:0000520Proptosis
HP:0000546Retinal degeneration
HP:0000586Shallow orbits

GWAS associations

2 associations (top):

StudyTraitp-value
GCST006143_7Bone mineral density (total hip)3.000000e-06
GCST010703_2Brain morphology (MOSTest)3.000000e-37

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007702hip bone mineral density
EFO:0004346neuroimaging measurement

MeSH disease descriptors (4)

DescriptorNameTree numbers
D007873Legg-Calve-Perthes DiseaseC05.116.852.175.570
D009081MucolipidosesC05.116.198.371; C10.228.140.163.100.435.590; C16.320.565.189.435.590; C16.320.565.202.670; C16.320.565.595.554.590; C18.452.132.100.435.590; C18.452.648.189.435.590; C18.452.648.202.670; C18.452.648.595.554.590
D012544Scheuermann DiseaseC05.116.821.500.500; C05.116.900.800.500.500; C05.116.900.808.500
C538602Mucolipidosis 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
Valproic Acidincreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
GSK-J4increases expression1
bisphenol Faffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression, increases methylation1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
potassium chromate(VI)decreases expression, affects cotreatment1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
bisphenol Sincreases methylation1
incobotulinumtoxinAincreases expression1
(+)-JQ1 compoundincreases expression1
Resveratrolaffects cotreatment, increases expression1
Ethanolincreases expression1
Cadmiumincreases abundance, increases expression1
Cisplatinincreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Diethylstilbestroldecreases expression1
Doxorubicinaffects response to substance1
Indomethacinaffects cotreatment, increases expression1
Plant Extractsaffects cotreatment, increases expression1
Polychlorinated Biphenylsaffects expression1
Quercetindecreases expression1
Ribonucleotidesaffects binding1

Cellosaurus cell lines

34 cell lines: 27 finite cell line, 3 transformed cell line, 3 cancer cell line, 1 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_9Q85GM00080Finite cell lineFemale
CVCL_9Q86GM00081Finite cell lineMale
CVCL_9Q87GM01586Finite cell lineMale
CVCL_9Q88GM01589Finite cell lineMale
CVCL_9Q89GM01590Finite cell lineFemale
CVCL_9Q90GM02273Finite cell lineMale
CVCL_9Q91GM02660Transformed cell lineFemale
CVCL_9Q92GM02687Transformed cell lineMale
CVCL_9Q93GM03066Finite cell lineFemale
CVCL_9R60GM00113Finite cell lineFemale

Clinical trials (associated diseases)

33 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04360265PHASE3ENROLLING_BY_INVITATIONFollow-up Study of AAV-Mediated Gene Transfer (UX111; Previously Known as ABO-102) for MPS Type IIIA
NCT00208468PHASE3TERMINATEDA Randomised Multi-centre Study to Compare the Long-term Performance of the Future Hip to 3 Other Implants in Primary Total Hip Replacement
NCT00176917PHASE2COMPLETEDStem Cell Transplantation for Hurler
NCT00383448PHASE2COMPLETEDHSCT for High Risk Inherited Inborn Errors
NCT06567769PHASE1RECRUITINGPhase 1 Study of GC1130A in Patients With Sanfilippo Syndrome Type A (MPS IIIA)
NCT00005900Not specifiedUNKNOWNStudy of Pulmonary Complications in Pediatric Patients With Storage Disorders Undergoing Allogeneic Hematopoietic Stem Cell Transplantation
NCT01891422Not specifiedCOMPLETEDLongitudinal Studies of the Glycoproteinoses
NCT02716246PHASE2/PHASE3RECRUITINGPhase I/II/III Gene Transfer Clinical Trial of scAAV9.U1a.hSGSH
NCT03612869PHASE2/PHASE3UNKNOWNStudy of AAVrh10-h.SGSH Gene Therapy in Patients With Mucopolysaccharidosis Type IIIA (MPS IIIA)
NCT03423186PHASE1/PHASE2COMPLETEDA Study to Assess the Safety and Tolerability of SOBI003 in Pediatric MPS IIIA Patients
NCT03811028PHASE1/PHASE2COMPLETEDA Study to Assess the Safety, Tolerability, and Efficacy of Long-term SOBI003 Treatment in Pediatric MPS IIIA Patients
NCT04088734PHASE1/PHASE2TERMINATEDGene Transfer Study of ABO-102 in Patients With Middle and Advanced Phases of MPS IIIA Disease
NCT04201405PHASE1/PHASE2ACTIVE_NOT_RECRUITINGGene Therapy with Modified Autologous Hematopoietic Stem Cells for Patients with Mucopolysaccharidosis Type IIIA
NCT06181136PHASE1/PHASE2ACTIVE_NOT_RECRUITINGStudy of DNL126 in Pediatric Participants With Mucopolysaccharidosis Type IIIA (Sanfilippo Syndrome Type A)
NCT01047306Not specifiedCOMPLETEDA Study of Patients With Sanfilippo Syndrome Type A (MPS IIIA)
NCT01873911Not specifiedCOMPLETEDNeurobehavioral Phenotypes in MPS III
NCT02037880Not specifiedCOMPLETEDNatural History Studies of Mucopolysaccharidosis III
NCT04918641Not specifiedUNKNOWNNatural History Observational Study of MPS IIIa in SMC
NCT01026909Not specifiedTERMINATEDIntraarticular Corticosteroid Therapy in Perthes Disease.
NCT02040714Not specifiedENROLLING_BY_INVITATIONMulticenter Prospective Cohort Study on Current Treatments of Legg-Calvé-Perthes Disease
NCT02087436Not specifiedCOMPLETEDTaperloc Complete Microplasty vs Taperloc Complete Standard: Randomized Controlled Study on Bone Mineral Density
NCT02087449Not specifiedTERMINATEDEvaluate E1 Wear, Clinical Performance of E1 Liner in THA in Korean Patient Population
NCT02676271Not specifiedCOMPLETEDThe Long Term Outcome of Varus Derotational Osteotomy for Legg-Calvé-Perthes’ Disease
NCT02795494Not specifiedUNKNOWNWOMAC Hip Score in Children and Adolescents With Perthes Disease
NCT03885960Not specifiedACTIVE_NOT_RECRUITINGPerthes Disease in Norway
NCT05734651Not specifiedRECRUITINGPROMIS Evaluation Study
NCT05840146Not specifiedCOMPLETEDKineesiotaping for Patients With LCPD
NCT06823089Not specifiedRECRUITINGEarly Feasibility Study of Cartilage Defect Repair
NCT07122323Not specifiedENROLLING_BY_INVITATIONRobotic Arm-assisted THA Vs. Conventional THA in Legg-Calvé-Perthes Disease
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT03851367Not specifiedCOMPLETEDSling Suspension Versus Gym Balls in the Treatment of Juvenile Spinal Osteochondrosis
NCT04924556Not specifiedUNKNOWNThe Effect of Rıgıd Brace on Spinopelvic Parameters and GAP Score in Adolescents With Structural Hyperkyphosis
NCT07117448Not specifiedCOMPLETEDClinical and Radiological Correlates of Balance, Pain and Body Image in Adolescents With Scheuermann’s Kyphosis