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POMK protein O-mannose kinase [ Homo sapiens (human) ]

Gene ID: 84197, updated on 3-Nov-2024

Summary

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Official Symbol
POMKprovided by HGNC
Official Full Name
protein O-mannose kinaseprovided by HGNC
Primary source
HGNC:HGNC:26267
See related
Ensembl:ENSG00000185900 MIM:615247; AllianceGenome:HGNC:26267
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
SGK196; MDDGA12; MDDGC12
Summary
This gene encodes a protein that may be involved in the presentation of the laminin-binding O-linked carbohydrate chain of alpha-dystroglycan (a-DG), which forms transmembrane linkages between the extracellular matrix and the exoskeleton. Some pathogens use this O-linked carbohydrate unit for host entry. Loss of function compound heterozygous mutations in this gene were found in a human patient affected by the Walker-Warburg syndrome (WWS) phenotype. Mice lacking this gene contain misplaced neurons (heterotopia) in some regions of the brain, possibly from defects in neuronal migration. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in brain (RPKM 2.1), testis (RPKM 1.7) and 25 other tissues See more
Orthologs
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Genomic context

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See POMK in Genome Data Viewer
Location:
8p11.21
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (43093515..43123434)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (43362447..43392367)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (42948658..42978577)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19161 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:42774215-42774934 Neighboring gene hook microtubule tethering protein 3 Neighboring gene MPRA-validated peak7007 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:42888473-42889024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27320 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19162 Neighboring gene RNA, U1 small nuclear 124, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27321 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42948529-42949434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:42947622-42948528 Neighboring gene farnesyltransferase, CAAX box, subunit alpha Neighboring gene NANOG hESC enhancer GRCh37_chr8:42971985-42972543 Neighboring gene Sharpr-MPRA regulatory region 5985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19164 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27322 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27324 Neighboring gene heparan-alpha-glucosaminide N-acetyltransferase Neighboring gene RNY5 pseudogene 6 Neighboring gene vomeronasal 1 receptor 45 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 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. Pathogenic homozygous variant in POMK gene is the cause of prenatally detected severe ventriculomegaly in two Lithuanian families. Preiksaitiene E, et al. Am J Med Genet A, 2020 Mar. PMID 31833209
  2. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. Jae LT, et al. Science, 2013 Apr 26. PMID 23519211, Free PMC Article
  3. POMK mutation in a family with congenital muscular dystrophy with merosin deficiency, hypomyelination, mild hearing deficit and intellectual disability. von Renesse A, et al. J Med Genet, 2014 Apr. PMID 24556084
  4. Emerging roles of pseudokinases. Boudeau J, et al. Trends Cell Biol, 2006 Sep. PMID 16879967
  5. POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations. Di Costanzo S, et al. Hum Mol Genet, 2014 Nov 1. PMID 24925318, Free PMC Article

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Pathogenic homozygous variant in POMK gene is the cause of prenatally detected severe ventriculomegaly in two Lithuanian families.
    Title: Pathogenic homozygous variant in POMK gene is the cause of prenatally detected severe ventriculomegaly in two Lithuanian families.
  2. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases.
    Title: Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases.
  3. POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations.
    Title: POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations.
  4. Homozygous truncating mutations in POMK lead to congenital muscular dystrophies with secondary merosin deficiency, hypomyelination and intellectual disability.
    Title: POMK mutation in a family with congenital muscular dystrophy with merosin deficiency, hypomyelination, mild hearing deficit and intellectual disability.
  5. These findings suggest how mutations in GTDC2, B3GALNT2, and SGK196 disrupt dystroglycan receptor function and lead to congenital muscular dystrophy.
    Title: SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function.
Submit: New GeneRIF Correction

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

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

  • FLJ23356, MGC126597

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables carbohydrate kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables carbohydrate kinase activity TAS
Traceable Author Statement
more info
  
enables phosphotransferase activity, alcohol group as acceptor IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphotransferase activity, alcohol group as acceptor IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in brain development TAS
Traceable Author Statement
more info
 PubMed 
involved_in carbohydrate phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in learning or memory IEA
Inferred from Electronic Annotation
more info
  
involved_in neuromuscular process IEA
Inferred from Electronic Annotation
more info
  
involved_in protein O-linked glycosylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein O-linked glycosylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein O-linked glycosylation TAS
Traceable Author Statement
more info
  
involved_in protein phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of pain IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
protein O-mannose kinase
Names
Sugen kinase 196
probable inactive protein kinase-like protein SgK196
protein kinase-like protein SgK196
NP_001264900.1
NP_115613.1

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_033235.1 RefSeqGene

    Range
    5010..34929
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001277971.2 → NP_001264900.1  protein O-mannose kinase

    See identical proteins and their annotated locations for NP_001264900.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC113191, BC113703, BQ365114, DA818523, EH337134
    Consensus CDS
    CCDS6141.1
    UniProtKB/Swiss-Prot
    Q9H5K3
    UniProtKB/TrEMBL
    A0A6Q8PFH3
    Related
    ENSP00000502774.1, ENST00000676193.1
    Conserved Domains (1) summary
    cd00180
    Location:88 → 329
    PKc; Catalytic domain of Protein Kinases

  2. NM_032237.5 → NP_115613.1  protein O-mannose kinase

    See identical proteins and their annotated locations for NP_115613.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC113191, BC101548, BQ365114, DA330953, EH337134
    Consensus CDS
    CCDS6141.1
    UniProtKB/Swiss-Prot
    Q9H5K3
    UniProtKB/TrEMBL
    A0A6Q8PFH3
    Related
    ENSP00000331258.5, ENST00000331373.10
    Conserved Domains (1) summary
    cd00180
    Location:88 → 329
    PKc; Catalytic domain of Protein Kinases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    43093515..43123434
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    43362447..43392367
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H5K3.1 GenPept UniProtKB/Swiss-Prot:Q9H5K3

Gene LinkOut

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