POMK (protein O-mannose kinase)

Gene

• Entrez ID: 84197
• Gene name: Protein O-mannose kinase
• Gene symbol: POMK
• Synonyms (NCBI Gene): MDDGA12, MDDGC12, SGK196
• Chromosome: 8
• Chromosome location: 8p11.21
• 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 u

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs143957574	A>G	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs149297443	A>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, missense variant
rs199756983	T>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs200555259	T>G	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs397509385	T>G	Pathogenic	Coding sequence variant, missense variant
rs397509386	A>G	Pathogenic	Coding sequence variant, missense variant
rs587777423	C>G,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs606231306	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs749980792	C>-,CC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs886041651	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1454006905	GA>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT741775	hsa-miR-548ao-3p	HITS-CLIP	23824327
MIRT741776	hsa-miR-451b	HITS-CLIP	23824327
MIRT741777	hsa-miR-6501-3p	HITS-CLIP	23824327
MIRT741778	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT741779	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT741780	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT741781	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT741782	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT741783	hsa-miR-4696	HITS-CLIP	23824327

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004672	Function	Protein kinase activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183, 32707033
GO:0005524	Function	ATP binding	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006493	Process	Protein O-linked glycosylation	IBA
GO:0006493	Process	Protein O-linked glycosylation	IDA	23929950
GO:0006493	Process	Protein O-linked glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	TAS
GO:0007420	Process	Brain development	IEA
GO:0007420	Process	Brain development	TAS	23929950
GO:0007611	Process	Learning or memory	IEA
GO:0016020	Component	Membrane	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016772	Function	Transferase activity, transferring phosphorus-containing groups	IEA
GO:0016773	Function	Phosphotransferase activity, alcohol group as acceptor	IBA
GO:0016773	Function	Phosphotransferase activity, alcohol group as acceptor	IDA	23929950
GO:0019200	Function	Carbohydrate kinase activity	IBA
GO:0019200	Function	Carbohydrate kinase activity	IEA
GO:0019200	Function	Carbohydrate kinase activity	TAS
GO:0019233	Process	Sensory perception of pain	IEA
GO:0046835	Process	Carbohydrate phosphorylation	IDA	23929950
GO:0046835	Process	Carbohydrate phosphorylation	IEA
GO:0050905	Process	Neuromuscular process	IEA

Other IDs

• MIM: 615247
• HGNC: 26267
• e!Ensembl: ENSG00000185900

Protein

• UniProt ID: Q9H5K3
• Protein name: Protein O-mannose kinase (POMK) (EC 2.7.1.183) (Protein kinase-like protein SgK196) (Sugen kinase 196)
• Protein 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-manno
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07714	PK_Tyr_Ser-Thr	81 → 218	Protein tyrosine and serine/threonine kinase	Domain

• Tissue specificity: TISSUE SPECIFICITY: Highest expression is observed in brain, skeletal muscle, kidney and heart in fetal and adult tissues. {ECO:0000269|PubMed:24925318}.
• Sequence:

  MEKQPQNSRRGLAPREVPPAVGLLLIMALMNTLLYLCLDHFFIAPRQSTVDPTHCPYGHF
  RIGQMKNCSPWLSCEELRTEVRQLKRVGEGAVKRVFLSEWKEHKVALSQLTSLEMKDDFL
  HGLQMLKSLQGTHVVTLLGYCEDDNTMLTEYHPLGSLSNLEETLNLSKYQNVNTWQHRLE
  LAMDYVSIINYLHHSPVGTRVMCDSNDLPKTLSQYLLTSNFSILANDLDALPLVNHSSGM
  LVKCGHRELHGDFVAPEQLWPYGEDVPFHDDLMPSYDEKIDIWKIPDISSFLLGHIEGSD
  MVRFHLFDIHKACKSQTPSERPTAQDVLETYQKVLDTLRDAMMSQAREML

• Sequence length: 350

Pathways

KEGG:

Mannose type O-glycan biosynthesis
Metabolic pathways

Reactome:

O-linked glycosylation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Limb-girdle muscular dystrophy due to POMK deficiency	Pathogenic; Likely pathogenic	rs781088854, rs774013796, rs2130601407, rs528307346, rs2130626422, rs587777423, rs2130626601, rs1251606511, rs751981817, rs2486780850, rs2486756300, rs1316985932, rs2486780804, rs2486781061, rs1586681137, rs1454006905, rs749980792, rs202006335, rs1206884841	RCV003781137 RCV001389788 RCV001384163 RCV001885168 RCV005225518 RCV000148014 RCV002035362 RCV003093439 RCV003088398 RCV002597218 RCV002824763 RCV005216088 RCV003798103 RCV003803928 RCV003805027 RCV000706836 RCV001203241 RCV001053386 RCV001221319	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12	Pathogenic; Likely pathogenic	rs781088854, rs774013796, rs2130601407, rs528307346, rs2130626422, rs587777423, rs2130626601, rs606231306, rs1251606511, rs751981817, rs2486780850, rs2486756300, rs1316985932, rs2486780804, rs2486781061, rs1586681137, rs1454006905, rs397509385, rs749980792, rs202006335, rs1206884841	RCV003781137 RCV001389788 RCV001384163 RCV001885168 RCV001825152 RCV000119846 RCV002035362 RCV000148015 RCV003093439 RCV003088398 RCV002597218 RCV002824763 RCV005216088 RCV003798103 RCV003803928 RCV003805027 RCV000706836 RCV000043555 RCV001203241 RCV001053386 RCV001221319	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
POMK-related disorder	Likely pathogenic; Pathogenic	rs2486780520, rs1316985932	RCV003392939 RCV003418852	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CONGENITAL MUSCULAR DYSTROPHY WITH CEREBELLAR INVOLVEMENT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MUSCLE EYE BRAIN DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WALKER-WARBURG CONGENITAL MUSCULAR DYSTROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WALKER-WARBURG SYNDROME	—	CTD, Orphanet CTD, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Absence of septum pellucidum	Absence Of Septum Pellucidum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
alpha-Dystroglycanopathies	alpha-Dystroglycanopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Anophthalmos	Syndromic microphthalmia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebellar Hypoplasia	Cerebellar Hypoplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cobblestone Lissencephaly	Cobblestone Lissencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32852072	Associate	★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Hydrocephalus	Congenital Hydrocephalus	BEFREE	31833209		★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of penis	Congenital Hypoplasia Of Penis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital keratoglobus	Congenital Keratoglobus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	GENOMICS_ENGLAND_DG	29910097		★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	BEFREE	31833209		★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy with cerebellar involvement	Congenital Muscular Dystrophy With Cerebellar Involvement	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Encephalocele	Encephalocele	Pubtator	32907597	Associate	★☆☆☆☆ Found in Text Mining only
Fukuyama Type Congenital Muscular Dystrophy	Fukuyama Type Congenital Muscular Dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	BEFREE	31833209		★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of the optic nerve	Hypoplasia Of The Optic Nerve	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	24925318		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Limb-girdle muscular dystrophy due to POMK deficiency	Limb-girdle muscular dystrophy	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Lung Diseases	Lung disease	Pubtator	32275906	Associate	★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	BEFREE	31833209		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macroglossia	Macroglossia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mirror movements disorder	Mirror Movements	BEFREE	28109637		★☆☆☆☆ Found in Text Mining only
Muscle eye brain disease	Muscle Eye Brain Disease	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	BEFREE	29910097, 31833209		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophies, Limb-Girdle	Limb-Girdle Muscular Dystrophy	GENOMICS_ENGLAND_DG	29910097		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K	Limb-girdle muscular dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy-Dystroglycanopathy (Congenital with Brain and Eye Anomalies) Type A, 1	Muscular Dystrophy-Dystroglycanopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 12	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	UNIPROT_DG	23519211, 23929950, 24556084, 24925318		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 12	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	GENOMICS_ENGLAND_DG	24556084, 24925318, 29910097		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH BRAIN AND EYE ANOMALIES), TYPE A, 12	Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	CLINVAR_DG	24556084, 24925318		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	CLINVAR_DG	24556084, 24925318		★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	ORPHANET_DG	24925318		★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	GENOMICS_ENGLAND_DG	29910097		★☆☆☆☆ Found in Text Mining only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 12	Limb-Girdle Muscular Dystrophy-Dystroglycanopathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neuronal heterotopia	Neuronal Heterotopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Occipital Encephalocele	Occipital Encephalocele	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Detachment	Retinal Detachment	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Retinal Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Retinal Dystrophies	Retinal Dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Small cell carcinoma of lung	Lung carcinoma	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Submucous cleft of hard palate	Submucosal cleft palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Vascular Remodeling	Vascular remodeling	Pubtator	32275906	Associate	★☆☆☆☆ Found in Text Mining only
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	ORPHANET_DG	23519211		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	BEFREE	24925318		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg congenital muscular dystrophy	Walker-Warburg Congenital Muscular Dystrophy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Walker-Warburg syndrome	Walker-Warburg Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations