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GNPTAB N-acetylglucosamine-1-phosphate transferase subunits alpha and beta [ Homo sapiens (human) ]

Gene ID: 79158, updated on 11-Apr-2024

Summary

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Official Symbol
GNPTABprovided by HGNC
Official Full Name
N-acetylglucosamine-1-phosphate transferase subunits alpha and betaprovided by HGNC
Primary source
HGNC:HGNC:29670
See related
Ensembl:ENSG00000111670 MIM:607840; AllianceGenome:HGNC:29670
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ICD; GNPTA
Summary
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.[provided by RefSeq, May 2010]
Expression
Ubiquitous expression in colon (RPKM 16.4), lung (RPKM 13.5) and 25 other tissues See more
Orthologs
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Genomic context

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See GNPTAB in Genome Data Viewer
Location:
12q23.2
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (101745499..101830959, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (101706726..101792185, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (102139277..102224737, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene choline phosphotransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6866 Neighboring gene uncharacterized LOC124902997 Neighboring gene synaptonemal complex protein 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_22731 Neighboring gene RNA, U6 small nuclear 101, pseudogene Neighboring gene ST13, Hsp70 interacting protein pseudogene 22 Neighboring gene RNA, 5S ribosomal pseudogene 368 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:102181608-102181804 Neighboring gene small nucleolar RNA U13 Neighboring gene RNA, U6 small nuclear 172, pseudogene Neighboring gene Sharpr-MPRA regulatory region 5955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4771 Neighboring gene RNA, 5S ribosomal pseudogene 369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:102248561-102249060 Neighboring gene CRISPRi-validated cis-regulatory element chr12.3153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6867 Neighboring gene RNA, U6 small nuclear 1183, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Structures of Bacterial MraY and Human GPT Provide Insights into Rational Antibiotic Design. Mashalidis EH, et al. J Mol Biol, 2020 Aug 21. PMID 32199982, Free PMC Article
  2. 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. Danyukova T, et al. Hum Mutat, 2020 Jan. PMID 31579991
  3. A genome-wide CRISPR screen identifies N-acetylglucosamine-1-phosphate transferase as a potential antiviral target for Ebola virus. Flint M, et al. Nat Commun, 2019 Jan 17. PMID 30655525, Free PMC Article
  4. MUCOLIPIDOSIS II INFANTS PRESENTING WITH SKELETAL DEFORMITIES MIMICKING RICKETS AND A NEW MUTATION IN GNPTAB GENE. Nur BG, et al. Genet Couns, 2016. PMID 30204966
  5. GNPTAB missense mutations cause loss of GlcNAc-1-phosphotransferase activity in mucolipidosis type II through distinct mechanisms. Ludwig NF, et al. Int J Biochem Cell Biol, 2017 Nov. PMID 28918368

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pathogenic variants in GNPTAB and GNPTG encoding distinct subunits of GlcNAc-1-phosphotransferase differentially impact bone resorption in patients with mucolipidosis type II and III.
    Title: Pathogenic variants in GNPTAB and GNPTG encoding distinct subunits of GlcNAc-1-phosphotransferase differentially impact bone resorption in patients with mucolipidosis type II and III.
  2. Disease-causing missense mutations within the N-terminal transmembrane domain of GlcNAc-1-phosphotransferase impair endoplasmic reticulum translocation or Golgi retention.
    Title: Disease-causing missense mutations within the N-terminal transmembrane domain of GlcNAc-1-phosphotransferase impair endoplasmic reticulum translocation or Golgi retention.
  3. Identification and characterization of 30 novel pathogenic variations in 69 unrelated Indian patients with Mucolipidosis Type II and Type III.
    Title: Identification and characterization of 30 novel pathogenic variations in 69 unrelated Indian patients with Mucolipidosis Type II and Type III.
  4. 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.
    Title: 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.
  5. Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?
    Title: Do Genes Associated with Dyslexia of Chinese Characters Evolve Neutrally?
  6. Structures of Bacterial MraY and Human GPT Provide Insights into Rational Antibiotic Design.
    Title: Structures of Bacterial MraY and Human GPT Provide Insights into Rational Antibiotic Design.
  7. 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.
    Title: Genetic factors and therapy outcomes in persistent developmental stuttering.
  8. 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.
    Title: Human GNPTAB stuttering mutations engineered into mice cause vocalization deficits and astrocyte pathology in the corpus callosum.
  9. 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.
    Title: The lysosomal storage disorders mucolipidosis type II, type III alpha/beta, and type III gamma: Update on GNPTAB and GNPTG mutations.
  10. 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.
    Title: A genome-wide CRISPR screen identifies N-acetylglucosamine-1-phosphate transferase as a potential antiviral target for Ebola virus.
Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Mucolipidosis type II
MedGen: C2673377 OMIM: 252500 GeneReviews: GNPTAB-Related Disorders
Compare labs
Pseudo-Hurler polydystrophy
MedGen: C0033788 OMIM: 252600 GeneReviews: GNPTAB-Related Disorders
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC4170, KIAA1208, DKFZp762B226

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in N-glycan processing to lysosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in N-glycan processing to lysosome IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in carbohydrate phosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in carbohydrate phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in lysosome organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in secretion of lysosomal enzymes IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
Names
GlcNAc phosphotransferase
N-acetylglucosamine-1-phosphate transferase alpha and beta subunits
UDP-N-acetylglucosamine-1-phosphotransferase subunits alpha/beta
UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosamine
glcNAc-1-phosphotransferase subunits alpha/beta
glucosamine (UDP-N-acetyl)-lysosomal-enzyme N-acetylglucosamine phosphotransferase
stealth protein GNPTAB
NP_077288.2
XP_006719656.1
XP_011537033.1
XP_054229177.1
XP_054229178.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021243.1 RefSeqGene

    Range
    4909..90369
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_024312.5 → NP_077288.2  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor

    See identical proteins and their annotated locations for NP_077288.2

    Status: REVIEWED

    Source sequence(s)
    AC063950, AM085438, BP276948
    Consensus CDS
    CCDS9088.1
    UniProtKB/Swiss-Prot
    A2RRQ9, Q3T906, Q3ZQK2, Q6IPW5, Q86TQ2, Q96N13, Q9ULL2
    Related
    ENSP00000299314.7, ENST00000299314.12
    Conserved Domains (6) summary
    pfam00066
    Location:435 → 469
    Notch; LNR domain
    pfam06464
    Location:699 → 814
    DMAP_binding; DMAP1-binding Domain
    pfam11380
    Location:322 → 429
    Stealth_CR2; Stealth protein CR2, conserved region 2
    pfam17101
    Location:73 → 101
    Stealth_CR1; Stealth protein CR1, conserved region 1
    pfam17102
    Location:955 → 1003
    Stealth_CR3; Stealth protein CR3, conserved region 3
    pfam17103
    Location:1138 → 1194
    Stealth_CR4; Stealth protein CR4, conserved region 4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    101745499..101830959 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538731.3 → XP_011537033.1  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1

    Conserved Domains (6) summary
    pfam00066
    Location:408 → 442
    Notch; LNR domain
    pfam06464
    Location:672 → 787
    DMAP_binding; DMAP1-binding Domain
    pfam11380
    Location:295 → 402
    Stealth_CR2; Stealth protein CR2, conserved region 2
    pfam17101
    Location:46 → 74
    Stealth_CR1; Stealth protein CR1, conserved region 1
    pfam17102
    Location:928 → 976
    Stealth_CR3; Stealth protein CR3, conserved region 3
    pfam17103
    Location:1111 → 1167
    Stealth_CR4; Stealth protein CR4, conserved region 4

  2. XM_006719593.4 → XP_006719656.1  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X2

    Conserved Domains (5) summary
    pfam00066
    Location:435 → 469
    Notch; LNR domain
    pfam06464
    Location:699 → 814
    DMAP_binding; DMAP1-binding Domain
    pfam11380
    Location:322 → 429
    Stealth_CR2; Stealth protein CR2, conserved region 2
    pfam17101
    Location:73 → 101
    Stealth_CR1; Stealth protein CR1, conserved region 1
    pfam17102
    Location:955 → 1003
    Stealth_CR3; Stealth protein CR3, conserved region 3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    101706726..101792185 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373202.1 → XP_054229177.1  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X1

  2. XM_054373203.1 → XP_054229178.1  N-acetylglucosamine-1-phosphotransferase subunits alpha/beta isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q3T906.1 GenPept UniProtKB/Swiss-Prot:Q3T906

Gene LinkOut

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