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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
    mouse all
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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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