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Aliases for POMK Gene

Aliases for POMK Gene

  • Protein-O-Mannose Kinase 2 3 5
  • Protein Kinase-Like Protein SgK196 3 4
  • Sugen Kinase 196 3 4
  • SGK196 3 4
  • Probable Inactive Protein Kinase-Like Protein SgK196 3
  • Protein O-Mannose Kinase 3
  • EC 2.7.1.183 4
  • MDDGA12 3
  • MDDGC12 3

External Ids for POMK Gene

Previous GeneCards Identifiers for POMK Gene

  • GC08P042949

Summaries for POMK Gene

Entrez Gene Summary for POMK Gene

  • 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]

GeneCards Summary for POMK Gene

POMK (Protein-O-Mannose Kinase) is a Protein Coding gene. Diseases associated with POMK include Muscular Dystrophy-Dystroglycanopathy , Type C, 12 and Muscular Dystrophy-Dystroglycanopathy , Type A, 12. Among its related pathways are O-linked glycosylation and Mannose type O-glycan biosynthesis. GO annotations related to this gene include transferase activity, transferring phosphorus-containing groups and phosphotransferase activity, alcohol group as acceptor.

UniProtKB/Swiss-Prot for POMK Gene

  • Protein O-mannose kinase that specifically mediates phosphorylation at the 6-position of an O-mannose of the trisaccharide (N-acetylgalactosamine (GalNAc)-beta-1,3-N-acetylglucosamine (GlcNAc)-beta-1,4-mannose) to generate phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-1,3-N-acetylglucosamine-beta-1,4-(phosphate-6-)mannose). Phosphorylated O-mannosyl trisaccharide is a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity. Only shows kinase activity when the GalNAc-beta-3-GlcNAc-beta-terminus is linked to the 4-position of O-mannose, suggesting that this disaccharide serves as the substrate recognition motif.

Additional gene information for POMK Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for POMK Gene

Genomics for POMK Gene

Regulatory Elements for POMK Gene

Enhancers for POMK Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H043054 1.2 ENCODE 10.8 -37.0 -36971 4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF207 IKBKB HGSNAT ENSG00000254165 HOOK3 ENSG00000254673 ENSG00000254198 RNF170 POMK THAP1 FNTA
GH08H042718 1.2 Ensembl ENCODE 10 -372.8 -372822 3.8 HDAC1 FOXA2 ARID4B SIN3A DMAP1 RFX5 TCF12 ZNF766 POLR3A FOS POMK CHRNB3 GC08M042718 LOC105379396 PIR44292
GH08H043162 1 Ensembl ENCODE 11.2 +69.7 69733 1.3 SMARCA5 TRIM22 EBF1 DPF2 BATF RELA SP1 BCL11A IKZF1 EED POMK FNTA RNY5P6 VN1R45P
GH08H043124 0.9 ENCODE 11.3 +31.4 31426 0.9 FOXA2 ARNT ZEB1 CHAMP1 ZNF155 TCF12 CBX5 GATA2 ZNF416 ZNF350 ENSG00000254165 IKBKB HGSNAT ENSG00000254198 AP3M2 POMK FNTA HOOK3 PIR36068 PIR33425
GH08H043159 0.8 ENCODE 11.3 +67.1 67106 2.2 CEBPG EBF1 BATF RELA EED ATF7 ETV6 RUNX3 IKZF2 CREM HGSNAT ENSG00000254198 POMK RNY5P6 VN1R45P
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around POMK on UCSC Golden Path with GeneCards custom track

Promoters for POMK Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000224166 -6 2601 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 CBX5 ZNF143 ZNF207 ZHX2

Genomic Locations for POMK Gene

Genomic Locations for POMK Gene
chr8:43,093,506-43,123,440
(GRCh38/hg38)
Size:
29,935 bases
Orientation:
Plus strand
chr8:42,948,657-42,978,577
(GRCh37/hg19)

Genomic View for POMK Gene

Genes around POMK on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POMK Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POMK Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POMK Gene

Proteins for POMK Gene

  • Protein details for POMK Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H5K3-SG196_HUMAN
    Recommended name:
    Protein O-mannose kinase
    Protein Accession:
    Q9H5K3

    Protein attributes for POMK Gene

    Size:
    350 amino acids
    Molecular mass:
    40050 Da
    Quaternary structure:
    No Data Available

neXtProt entry for POMK Gene

Post-translational modifications for POMK Gene

  • Ubiquitination at Lys3
  • Glycosylation at posLast=165165, Asn220, and Asn235
  • Modification sites at PhosphoSitePlus

Other Protein References for POMK Gene

No data available for DME Specific Peptides for POMK Gene

Domains & Families for POMK Gene

Gene Families for POMK Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted membrane proteins

Protein Domains for POMK Gene

Suggested Antigen Peptide Sequences for POMK Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H5K3

UniProtKB/Swiss-Prot:

SG196_HUMAN :
  • Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. STKL subfamily.
Family:
  • Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. STKL subfamily.
genes like me logo Genes that share domains with POMK: view

Function for POMK Gene

Molecular function for POMK Gene

UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=4.1 uM for ATP {ECO:0000269 PubMed:23929950};
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + O(3)-(N-acetyl-beta-D-galactosaminyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->4)-alpha-D-mannosyl)-L-threonyl/L-seryl-[protein] = ADP + O(3)-(N-acetyl-beta-D-galactosaminyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->4)-alpha-D-(6-phospho)mannosyl)-L-threonyl/L-seryl-[protein].
UniProtKB/Swiss-Prot Function:
Protein O-mannose kinase that specifically mediates phosphorylation at the 6-position of an O-mannose of the trisaccharide (N-acetylgalactosamine (GalNAc)-beta-1,3-N-acetylglucosamine (GlcNAc)-beta-1,4-mannose) to generate phosphorylated O-mannosyl trisaccharide (N-acetylgalactosamine-beta-1,3-N-acetylglucosamine-beta-1,4-(phosphate-6-)mannose). Phosphorylated O-mannosyl trisaccharide is a carbohydrate structure present in alpha-dystroglycan (DAG1), which is required for binding laminin G-like domain-containing extracellular proteins with high affinity. Only shows kinase activity when the GalNAc-beta-3-GlcNAc-beta-terminus is linked to the 4-position of O-mannose, suggesting that this disaccharide serves as the substrate recognition motif.

Enzyme Numbers (IUBMB) for POMK Gene

Gene Ontology (GO) - Molecular Function for POMK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004672 protein kinase activity IEA --
GO:0005524 ATP binding IEA --
GO:0016301 kinase activity IEA --
GO:0016740 transferase activity IEA --
GO:0016773 phosphotransferase activity, alcohol group as acceptor IDA 23929950
genes like me logo Genes that share ontologies with POMK: view
genes like me logo Genes that share phenotypes with POMK: view

Human Phenotype Ontology for POMK Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for POMK Gene

miRTarBase miRNAs that target POMK

Inhibitory RNA Products

No data available for Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for POMK Gene

Localization for POMK Gene

Subcellular locations from UniProtKB/Swiss-Prot for POMK Gene

Endoplasmic reticulum membrane; Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for POMK gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 3
cytosol 2
golgi apparatus 2
plasma membrane 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for POMK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with POMK: view

Pathways & Interactions for POMK Gene

genes like me logo Genes that share pathways with POMK: view

Pathways by source for POMK Gene

Gene Ontology (GO) - Biological Process for POMK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration IEA --
GO:0006468 protein phosphorylation IEA --
GO:0006493 protein O-linked glycosylation TAS --
GO:0007420 brain development TAS 23929950
GO:0007611 learning or memory IEA --
genes like me logo Genes that share ontologies with POMK: view

No data available for SIGNOR curated interactions for POMK Gene

Drugs & Compounds for POMK Gene

No Compound Related Data Available

Transcripts for POMK Gene

mRNA/cDNA for POMK Gene

(2) REFSEQ mRNAs :
(12) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for POMK Gene

No ASD Table

Relevant External Links for POMK Gene

GeneLoc Exon Structure for
POMK
ECgene alternative splicing isoforms for
POMK

Expression for POMK Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for POMK Gene

Protein differential expression in normal tissues from HIPED for POMK Gene

This gene is overexpressed in Fetal Brain (26.5), Placenta (20.2), Testis (15.0), and Frontal cortex (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for POMK Gene



Protein tissue co-expression partners for POMK Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of POMK Gene:

POMK

mRNA Expression by UniProt/SwissProt for POMK Gene:

Q9H5K3-SG196_HUMAN
Tissue specificity: Highest expression is observed in brain, skeletal muscle, kidney and heart in fetal and adult tissues.

Evidence on tissue expression from TISSUES for POMK Gene

  • Nervous system(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for POMK Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pituitary gland
  • skull
  • tongue
Thorax:
  • breast
  • chest wall
  • clavicle
  • heart
  • heart valve
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • kidney
  • large intestine
Pelvis:
  • anus
  • ovary
  • pelvis
  • penis
  • prostate
  • rectum
  • testicle
  • ureter
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with POMK: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for POMK Gene

Orthologs for POMK Gene

This gene was present in the common ancestor of chordates.

Orthologs for POMK Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia POMK 34
  • 100 (a)
OneToOne
SGK196 33
  • 99.52 (n)
dog
(Canis familiaris)
Mammalia SGK196 33
  • 83.62 (n)
POMK 34
  • 80 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pomk 33 16 34
  • 80.69 (n)
rat
(Rattus norvegicus)
Mammalia Pomk 33
  • 79.63 (n)
cow
(Bos Taurus)
Mammalia LOC514490 33
  • 77.33 (n)
POMK 34
  • 77 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia POMK 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia POMK 34
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves SGK196 33 34
  • 69.33 (n)
lizard
(Anolis carolinensis)
Reptilia POMK 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100497421 33
  • 64.53 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.4020 33
zebrafish
(Danio rerio)
Actinopterygii pomk 33 34
  • 59.51 (n)
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8442 33
Species where no ortholog for POMK was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for POMK Gene

ENSEMBL:
Gene Tree for POMK (if available)
TreeFam:
Gene Tree for POMK (if available)

Paralogs for POMK Gene

Pseudogenes.org Pseudogenes for POMK Gene

genes like me logo Genes that share paralogs with POMK: view

No data available for Paralogs for POMK Gene

Variants for POMK Gene

Sequence variations from dbSNP and Humsavar for POMK Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs199756983 Pathogenic, Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A12 (MDDGA12) [MIM:615249] 43,122,729(+) TATGG(A/T)CCGAT reference, missense
rs397509385 Pathogenic, Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A12 (MDDGA12) [MIM:615249] 43,122,234(+) CACGC(G/T)GCTTG reference, missense
rs397509386 Pathogenic, Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A12 (MDDGA12) [MIM:615249] 43,122,597(+) AGAGC(A/G)ACTGT reference, missense
VAR_041376 A lung small cell carcinoma sample
rs587777423 Pathogenic 43,122,149(+) TCTCA(C/G/T)AGCTC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for POMK Gene

Variant ID Type Subtype PubMed ID
nsv831302 CNV loss 17160897
nsv477416 CNV novel sequence insertion 20440878
nsv470208 CNV gain 18288195
nsv1032781 CNV gain 25217958
esv3891387 CNV gain 25118596
esv3617027 CNV gain 21293372
esv3617026 CNV gain 21293372
dgv7187n100 CNV gain 25217958

Variation tolerance for POMK Gene

Residual Variation Intolerance Score: 61.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.89; 48.61% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for POMK Gene

Human Gene Mutation Database (HGMD)
POMK
SNPedia medical, phenotypic, and genealogical associations of SNPs for
POMK

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POMK Gene

Disorders for POMK Gene

MalaCards: The human disease database

(9) MalaCards diseases for POMK Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
muscular dystrophy-dystroglycanopathy , type c, 12
  • muscular dystrophy-dystroglycanopathy , type c 12
muscular dystrophy-dystroglycanopathy , type a, 12
  • muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies a12
congenital muscular dystrophy-dystroglycanopathy with brain and eye anomalies type a 12
  • muscular dystrophy-dystroglycanopathy , type a, 12
congenital muscular dystrophy with cerebellar involvement
  • cmd with cerebellar involvement
walker-warburg syndrome
  • cerebroocular dysplasia-muscular dystrophy syndrome
- elite association - COSMIC cancer census association via MalaCards
Search POMK in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SG196_HUMAN
  • Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A12 (MDDGA12) [MIM:615249]: An autosomal recessive disorder characterized by congenital muscular dystrophy associated with cobblestone lissencephaly and other brain anomalies, eye malformations, profound mental retardation, and death usually in the first years of life. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease. {ECO:0000269 PubMed:23519211, ECO:0000269 PubMed:23929950, ECO:0000269 PubMed:24556084, ECO:0000269 PubMed:24925318}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Muscular dystrophy-dystroglycanopathy limb-girdle C12 (MDDGC12) [MIM:616094]: An autosomal recessive limb-girdle congenital muscular dystrophy, characterized by muscle weakness and delayed motor development in association with cognitive impairment. {ECO:0000269 PubMed:24925318}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for POMK

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
POMK
genes like me logo Genes that share disorders with POMK: view

No data available for Genatlas for POMK Gene

Publications for POMK Gene

  1. Deciphering the glycosylome of dystroglycanopathies using haploid screens for lassa virus entry. (PMID: 23519211) Jae LT … Brummelkamp TR (Science (New York, N.Y.) 2013) 2 3 4 60
  2. POMK mutation in a family with congenital muscular dystrophy with merosin deficiency, hypomyelination, mild hearing deficit and intellectual disability. (PMID: 24556084) von Renesse A … Schuelke M (Journal of medical genetics 2014) 3 4 60
  3. POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations. (PMID: 24925318) Di Costanzo S … Manzini MC (Human molecular genetics 2014) 3 4 60
  4. SGK196 is a glycosylation-specific O-mannose kinase required for dystroglycan function. (PMID: 23929950) Yoshida-Moriguchi T … Campbell KP (Science (New York, N.Y.) 2013) 3 4 60
  5. Emerging roles of pseudokinases. (PMID: 16879967) Boudeau J … Alessi DR (Trends in cell biology 2006) 2 3 60

Products for POMK Gene

  • Addgene plasmids for POMK

Sources for POMK Gene

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