POMK

Summary

POMK (protein O-mannose kinase, HGNC:26267) is a protein-coding gene on chromosome 8p11.21, encoding Protein O-mannose kinase (Q9H5K3). 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-acetylgalacto….

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.

Source: NCBI Gene 84197 — RefSeq curated summary.

At a glance

• Gene–disease (curated): muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12 (Definitive, GenCC) — +4 more curated relationships
• GWAS associations: 1
• Clinical variants (ClinVar): 290 total — 21 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 111
• MANE Select transcript: NM_032237

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26267
Approved symbol	POMK
Name	protein O-mannose kinase
Location	8p11.21
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23356, SgK196
Ensembl gene	ENSG00000185900
Ensembl biotype	protein_coding
OMIM	615247
Entrez	84197

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 9 protein_coding, 6 protein_coding_CDS_not_defined, 5 nonsense_mediated_decay, 1 retained_intron

ENST00000331373, ENST00000518991, ENST00000614426, ENST00000674646, ENST00000674676, ENST00000674727, ENST00000674782, ENST00000674820, ENST00000674937, ENST00000675013, ENST00000675129, ENST00000675322, ENST00000675501, ENST00000675509, ENST00000675675, ENST00000675791, ENST00000676163, ENST00000676178, ENST00000676193, ENST00000676356, ENST00000936358

RefSeq mRNA: 2 — MANE Select: NM_032237 NM_001277971, NM_032237

CCDS: CCDS6141

Canonical transcript exons

ENST00000331373 — 5 exons

Exon	Start	End
ENSE00001302767	43122107	43123434
ENSE00001325776	43103528	43103830
ENSE00001526423	43102505	43102600
ENSE00001526424	43097524	43097615
ENSE00001526426	43093515	43093563

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 95.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.3681 / max 143.1427, expressed in 1792 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
88717	12.7158	1787
88716	0.6522	382

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
paraflocculus	UBERON:0005351	95.50	gold quality
middle temporal gyrus	UBERON:0002771	95.00	gold quality
Brodmann (1909) area 10	UBERON:0013541	94.80	gold quality
frontal pole	UBERON:0002795	94.54	gold quality
cerebellar vermis	UBERON:0004720	94.28	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.84	gold quality
adult organism	UBERON:0007023	93.07	gold quality
middle frontal gyrus	UBERON:0002702	92.92	gold quality
lateral nuclear group of thalamus	UBERON:0002736	92.35	gold quality
entorhinal cortex	UBERON:0002728	92.23	gold quality
postcentral gyrus	UBERON:0002581	91.92	gold quality
endometrium epithelium	UBERON:0004811	91.86	gold quality
parietal lobe	UBERON:0001872	91.74	gold quality
substantia nigra pars compacta	UBERON:0001965	90.94	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.69	gold quality
hair follicle	UBERON:0002073	90.66	gold quality
CA1 field of hippocampus	UBERON:0003881	90.48	gold quality
tongue squamous epithelium	UBERON:0006919	90.42	gold quality
esophagus squamous epithelium	UBERON:0006920	90.36	gold quality
upper leg skin	UBERON:0004262	90.14	gold quality
tibia	UBERON:0000979	89.86	gold quality
visceral pleura	UBERON:0002401	89.83	gold quality
orbitofrontal cortex	UBERON:0004167	89.80	gold quality
epithelium of esophagus	UBERON:0001976	89.42	gold quality
superior frontal gyrus	UBERON:0002661	89.41	gold quality
substantia nigra pars reticulata	UBERON:0001966	89.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.51	gold quality
squamous epithelium	UBERON:0006914	88.44	gold quality
dorsal root ganglion	UBERON:0000044	88.41	gold quality
oral cavity	UBERON:0000167	88.24	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting POMK, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-6134	99.63	65.68	1537
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-6878-5P	98.49	67.91	2142
HSA-MIR-3138	98.41	67.53	744
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-4800-5P	97.22	65.91	324
HSA-MIR-4491	96.53	66.20	935
HSA-MIR-4657	96.53	66.57	895

Literature-anchored findings (GeneRIF, showing 5)

• These findings suggest how mutations in GTDC2, B3GALNT2, and SGK196 disrupt dystroglycan receptor function and lead to congenital muscular dystrophy. (PMID:23929950)
• Homozygous truncating mutations in POMK lead to congenital muscular dystrophies with secondary merosin deficiency, hypomyelination and intellectual disability. (PMID:24556084)
• POMK mutations disrupt muscle development leading to a spectrum of neuromuscular presentations. (PMID:24925318)
• Pathogenic homozygous variant in POMK gene is the cause of prenatally detected severe ventriculomegaly in two Lithuanian families. (PMID:31833209)
• Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. (PMID:32707033)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pomk	ENSDARG00000003208
mus_musculus	Pomk	ENSMUSG00000037251
rattus_norvegicus	Pomk	ENSRNOG00000014628

Protein

Protein identifiers

Protein O-mannose kinase — Q9H5K3 (reviewed: Q9H5K3)

Alternative names: Protein kinase-like protein SgK196, Sugen kinase 196

All UniProt accessions (6): A0A6Q8PF73, A0A6Q8PFG8, A0A6Q8PFH3, A0A6Q8PFX5, E5RJD5, Q9H5K3

UniProt curated annotations — full annotation on UniProt →

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.

Subcellular location. Endoplasmic reticulum membrane.

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

Disease relevance. 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 intellectual disability, 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. The disease is caused by variants 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. STKL subfamily.

RefSeq proteins (2): NP_001264900, NP_115613* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000719	Prot_kinase_dom	Domain
IPR001245	Ser-Thr/Tyr_kinase_cat_dom	Domain
IPR011009	Kinase-like_dom_sf	Homologous_superfamily
IPR039318	POMK	Family

Pfam: PF07714

Enzyme classification (BRENDA):

• EC 2.7.1.183 — glycoprotein-mannosyl O6-kinase (BRENDA: 3 organisms, 5 substrates, 0 inhibitors, 1 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ATP	0.0041	1

Catalyzed reactions (Rhea), 1 shown:

• 3-O-[beta-D-GalNAc-(1->3)-beta-D-GlcNAc-(1->4)-alpha-D-Man]-L-Thr-[protein] + ATP = 3-O-[beta-D-GalNAc-(1->3)-beta-D-GlcNAc-(1->4)-(O-6-P-alpha-D-Man)]-Thr-[protein] + ADP + H(+) (RHEA:52616)

UniProt features (17 total): sequence variant 8, glycosylation site 3, topological domain 2, chain 1, transmembrane region 1, domain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H5K3-F1	91.62	0.83

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 1

Glycosylation sites (3): 165, 220, 235

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-8932505	DAG1 core M3 glycosylations
R-HSA-392499	Metabolism of proteins
R-HSA-5173105	O-linked glycosylation
R-HSA-597592	Post-translational protein modification

MSigDB gene sets: 239 (showing top): BORCZUK_MALIGNANT_MESOTHELIOMA_UP, GOBP_COGNITION, GOBP_BEHAVIOR, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CARBOHYDRATE_PHOSPHORYLATION, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_SENSORY_PERCEPTION_OF_PAIN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_METABOLIC_PROCESS, LIAO_METASTASIS, GOBP_HEAD_DEVELOPMENT, DODD_NASOPHARYNGEAL_CARCINOMA_UP

GO Biological Process (7): protein O-linked glycosylation (GO:0006493), brain development (GO:0007420), learning or memory (GO:0007611), sensory perception of pain (GO:0019233), carbohydrate phosphorylation (GO:0046835), neuromuscular process (GO:0050905), protein phosphorylation (GO:0006468)

GO Molecular Function (10): protein kinase activity (GO:0004672), ATP binding (GO:0005524), phosphotransferase activity, alcohol group as acceptor (GO:0016773), mannokinase activity (GO:0019158), carbohydrate kinase activity (GO:0019200), nucleotide binding (GO:0000166), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740), transferase activity, transferring phosphorus-containing groups (GO:0016772)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum (GO:0005783), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
DAG1 glycosylations	1
Post-translational protein modification	1
Metabolism of proteins	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phosphorylation	2
kinase activity	2
transferase activity, transferring phosphorus-containing groups	2
cellular anatomical structure	2
glycoprotein biosynthetic process	1
central nervous system development	1
animal organ development	1
head development	1
behavior	1
cognition	1
sensory perception	1
carbohydrate metabolic process	1
nervous system process	1
protein modification process	1
phosphotransferase activity, alcohol group as acceptor	1
catalytic activity, acting on a protein	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
hexokinase activity	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
catalytic activity	1
transferase activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

798 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POMK	POMGNT2	Q8NAT1	892
POMK	B3GALNT2	Q8NCR0	881
POMK	RXYLT1	Q9Y2B1	877
POMK	POMT1	Q9Y6A1	847
POMK	FKTN	O75072	846
POMK	POMT2	Q9UKY4	846
POMK	B4GAT1	O43505	845
POMK	FKRP	Q9H9S5	845
POMK	POMGNT1	Q8WZA1	831
POMK	GMPPB	Q9Y5P6	789
POMK	DPM2	O94777	742
POMK	DPM1	O60762	736
POMK	DPM3	Q9P2X0	733
POMK	DOLK	Q9UPQ8	727
POMK	LARGE1	O95461	724

IntAct

78 interactions, top by confidence:

A	B	Type	Score
DSN1	NDC80	psi-mi:“MI:0914”(association)	0.790
POMK	LRP5	psi-mi:“MI:0914”(association)	0.640
POMK	IER3IP1	psi-mi:“MI:0915”(physical association)	0.560
MS4A13	POMK	psi-mi:“MI:0915”(physical association)	0.560
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
C3AR1	TMEM120B	psi-mi:“MI:0914”(association)	0.530
GPR21	TMEM120B	psi-mi:“MI:0914”(association)	0.530
POMK	TMEM120B	psi-mi:“MI:0914”(association)	0.530
ADGRG5	KLRG2	psi-mi:“MI:0914”(association)	0.530
GHITM	CCNB2	psi-mi:“MI:0914”(association)	0.530
MME	TMEM223	psi-mi:“MI:0914”(association)	0.530
FBXO2	TMEM131L	psi-mi:“MI:0914”(association)	0.530
A4GNT	POTEF	psi-mi:“MI:0914”(association)	0.530
POMK	CLGN	psi-mi:“MI:0914”(association)	0.530
FLVCR1	TNFRSF10B	psi-mi:“MI:0914”(association)	0.530
STT3A	POMK	psi-mi:“MI:0915”(physical association)	0.500
POMK	RPN2	psi-mi:“MI:0915”(physical association)	0.500
B3GAT3	POMK	psi-mi:“MI:0915”(physical association)	0.500
POMGNT1	POMK	psi-mi:“MI:0915”(physical association)	0.500
RPN1	POMK	psi-mi:“MI:0915”(physical association)	0.500
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
VIPR2	C15orf61	psi-mi:“MI:0914”(association)	0.350

BioGRID (375): CERS2 (Affinity Capture-MS), MBOAT7 (Affinity Capture-MS), GOLGA5 (Affinity Capture-MS), CANX (Affinity Capture-MS), LRP5 (Affinity Capture-MS), LRP6 (Affinity Capture-MS), GOLIM4 (Affinity Capture-MS), GHITM (Affinity Capture-MS), BRIP1 (Affinity Capture-MS), XYLT2 (Affinity Capture-MS), TMEM246 (Affinity Capture-MS), POMGNT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), TYW1B (Affinity Capture-MS), MOCS3 (Affinity Capture-MS)

ESM2 similar proteins: A0JPE1, A4D0V7, D3Z2R5, O43916, P97259, Q08834, Q09328, Q1RLQ5, Q3TUA9, Q4V8A9, Q58CX7, Q5F349, Q5FVL3, Q5HZP7, Q5NDE4, Q5NDE5, Q5NDE7, Q5NDE8, Q5R634, Q5R9Q9, Q5RJQ0, Q5T7M9, Q5U3W1, Q5VUD6, Q640M6, Q68CR1, Q6DBY9, Q6DCL6, Q6Q2W4, Q80TS8, Q8C1F4, Q8C3I9, Q8N6G5, Q8NBP0, Q8NHY0, Q8R4G6, Q8R553, Q8WTR4, Q92179, Q95JJ0

Diamond homologs: C0LGD8, Q3E8W4, Q3TUA9, Q4V8A9, Q5F349, Q5HZP7, Q5U3W1, Q5WA76, Q8S8S7, Q95JJ0, Q9FID8, Q9H5K3, Q9LRY1, Q9SR05, Q9LMN6, Q9LMN7, Q2R560, Q9FIJ6, Q9LY50, Q9LDZ5, Q9S9M5, Q54I36, Q8L4H4, Q8LKZ1, A0A5J5NT52, Q9FID9, Q9SFT7, A0A5J5T2N2, P0DKI6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 99 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
G alpha (s) signalling events	6	6.9×	1e-02
Neutrophil degranulation	12	4.3×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
adenylate cyclase-modulating G protein-coupled receptor signaling pathway	5	18.7×	1e-03
adenylate cyclase-activating G protein-coupled receptor signaling pathway	8	10.1×	4e-04
cell surface receptor signaling pathway	10	7.1×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

290 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	21
Likely pathogenic	1
Uncertain significance	151
Likely benign	84
Benign	8

Top pathogenic / likely-pathogenic (22)

Variant ID	HGVS	Classification
1071646	NM_032237.5(POMK):c.152del (p.Asp51fs)	Pathogenic
1076046	NM_032237.5(POMK):c.43C>T (p.Arg15Ter)	Pathogenic
133346	NM_032237.5(POMK):c.325C>T (p.Gln109Ter)	Pathogenic
1451698	NM_032237.5(POMK):c.452_455dup (p.His152fs)	Pathogenic
160348	NM_032237.5(POMK):c.288del (p.Leu97fs)	Pathogenic
1911792	NM_032237.5(POMK):c.754dup (p.Asp252fs)	Pathogenic
2002655	NM_032237.5(POMK):c.280A>T (p.Arg94Ter)	Pathogenic
2158045	NM_032237.5(POMK):c.94_98del (p.Thr32fs)	Pathogenic
2165161	NM_032237.5(POMK):c.247C>T (p.Gln83Ter)	Pathogenic
280444	NM_032237.5(POMK):c.917dup (p.Leu306fs)	Pathogenic
2926947	NM_032237.5(POMK):c.459del (p.Pro153_Leu154insTer)	Pathogenic
2932937	NM_032237.5(POMK):c.724dup (p.Val242fs)	Pathogenic
2945834	NM_032237.5(POMK):c.847del (p.Trp283fs)	Pathogenic
2951325	NM_032237.5(POMK):c.645T>G (p.Tyr215Ter)	Pathogenic
3752434	NM_032237.5(POMK):c.61del (p.Val21fs)	Pathogenic
3760619	NM_032237.5(POMK):c.91_98dup (p.Leu34fs)	Pathogenic
4791932	NM_032237.5(POMK):c.43del (p.Arg15fs)	Pathogenic
50610	NM_032237.5(POMK):c.410T>G (p.Leu137Arg)	Pathogenic
582702	NM_032237.5(POMK):c.238_239del (p.Glu80fs)	Pathogenic
651249	NC_000008.11:g.(?43103539)(43103840_?)del	Pathogenic
949777	NM_032237.5(POMK):c.282+1G>C	Pathogenic
2635081	NM_032237.5(POMK):c.615dup (p.Asn206fs)	Likely pathogenic

SpliceAI

731 predictions. Top by Δscore:

Variant	Effect	Δscore
8:43097504:T:TA	acceptor_gain	1.0000
8:43097506:T:TA	acceptor_gain	1.0000
8:43097508:T:TA	acceptor_gain	1.0000
8:43097510:T:TA	acceptor_gain	1.0000
8:43097516:A:AG	acceptor_gain	1.0000
8:43103523:TTTA:T	acceptor_loss	1.0000
8:43103527:G:GC	acceptor_loss	1.0000
8:43103827:GAGA:G	donor_gain	1.0000
8:43103526:A:AG	acceptor_gain	0.9900
8:43103526:AG:A	acceptor_gain	0.9900
8:43103527:G:GG	acceptor_gain	0.9900
8:43103527:GG:G	acceptor_gain	0.9900
8:43103527:GGA:G	acceptor_gain	0.9900
8:43103527:GGAA:G	acceptor_gain	0.9900
8:43103527:GGAAA:G	acceptor_gain	0.9900
8:43103786:G:GT	donor_gain	0.9900
8:43103786:GAA:G	donor_gain	0.9900
8:43103813:G:GT	donor_gain	0.9900
8:43103813:G:T	donor_gain	0.9900
8:43103829:GA:G	donor_gain	0.9900
8:43103831:G:GG	donor_gain	0.9900
8:43122103:GCAGG:G	acceptor_loss	0.9900
8:43122104:CAGGT:C	acceptor_loss	0.9900
8:43122105:A:AC	acceptor_loss	0.9900
8:43122106:G:GC	acceptor_loss	0.9900
8:43093562:AG:A	donor_loss	0.9800
8:43093563:GGTA:G	donor_loss	0.9800
8:43093565:T:G	donor_loss	0.9800
8:43097517:C:G	acceptor_gain	0.9800
8:43103525:TAGG:T	acceptor_gain	0.9800

AlphaMissense

2317 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:43122787:A:C	R321S	0.994
8:43122787:A:T	R321S	0.994
8:43122504:A:T	D227V	0.993
8:43122786:G:C	R321T	0.991
8:43103827:G:C	K93N	0.990
8:43103827:G:T	K93N	0.990
8:43122504:A:C	D227A	0.990
8:43122505:C:A	D227E	0.989
8:43122505:C:G	D227E	0.989
8:43122431:T:A	C203S	0.987
8:43122432:G:C	C203S	0.987
8:43122763:C:G	C313W	0.987
8:43122426:T:A	V201D	0.986
8:43122761:T:C	C313R	0.985
8:43122762:G:A	C313Y	0.984
8:43122471:T:C	L216P	0.983
8:43122504:A:G	D227G	0.983
8:43122360:T:C	L179P	0.982
8:43122401:C:G	H193D	0.982
8:43122432:G:A	C203Y	0.982
8:43122815:T:G	Y331D	0.982
8:43122435:A:T	D204V	0.981
8:43103726:T:C	F60L	0.980
8:43103728:C:A	F60L	0.980
8:43103728:C:G	F60L	0.980
8:43122436:C:A	D204E	0.980
8:43122436:C:G	D204E	0.980
8:43122467:T:G	Y215D	0.980
8:43122554:T:A	C244S	0.980
8:43122555:G:C	C244S	0.980

dbSNP variants (sampled 300 via entrez): RS1000100547 (8:43097677 T>C,G), RS1000147708 (8:43114444 G>A,T), RS1000159109 (8:43114338 C>T), RS1000310234 (8:43119375 T>C), RS1000361188 (8:43110669 G>A,T), RS1000413453 (8:43103874 G>A), RS1000497806 (8:43113575 G>A), RS1000549984 (8:43118420 A>G), RS1000728239 (8:43118313 A>G), RS1001066275 (8:43092327 C>A,T), RS1001088722 (8:43097918 G>A,C), RS1001091764 (8:43104692 C>G,T), RS1001297831 (8:43114125 C>T), RS1001351699 (8:43092084 T>C), RS1001489858 (8:43119074 G>A)

Disease associations

OMIM: gene MIM:615247 | disease phenotypes: MIM:615249, MIM:616094

GenCC curated gene-disease

Disease	Classification	Inheritance
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12	Definitive	Autosomal recessive
congenital muscular dystrophy with cerebellar involvement	Supportive	Autosomal recessive
limb-girdle muscular dystrophy due to POMK deficiency	Supportive	Autosomal recessive
muscular dystrophy-dystroglycanopathy, type A	Supportive	Autosomal recessive
anterior segment dysgenesis	Limited	Autosomal dominant

Mondo (5): muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 12 (MONDO:0014101), limb-girdle muscular dystrophy due to POMK deficiency (MONDO:0014489), (MONDO:0018277), muscular dystrophy-dystroglycanopathy, type A (MONDO:0000171), anterior segment dysgenesis (MONDO:0019503)

Orphanet (2): Limb-girdle muscular dystrophy due to POMK deficiency (Orphanet:445110), Walker-Warburg syndrome (Orphanet:899)

HPO phenotypes

111 total (30 of 111 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000158	Macroglossia
HP:0000175	Cleft palate
HP:0000176	Submucous cleft hard palate
HP:0000193	Bifid uvula
HP:0000238	Hydrocephalus
HP:0000252	Microcephaly
HP:0000253	Progressive microcephaly
HP:0000256	Macrocephaly
HP:0000358	Posteriorly rotated ears
HP:0000369	Low-set ears
HP:0000407	Sensorineural hearing impairment
HP:0000411	Protruding ear
HP:0000482	Microcornea
HP:0000485	Megalocornea
HP:0000486	Strabismus
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000518	Cataract
HP:0000525	Abnormality iris morphology
HP:0000528	Anophthalmia
HP:0000541	Retinal detachment
HP:0000545	Myopia
HP:0000546	Retinal degeneration
HP:0000556	Retinal dystrophy
HP:0000568	Microphthalmia
HP:0000587	Abnormal optic nerve morphology
HP:0000589	Coloboma
HP:0000609	Optic nerve hypoplasia

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002409_43	Childhood body mass index	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D058494	Walker-Warburg Syndrome	C10.500.507.450.499.249.500; C11.270.881; C16.131.666.507.450.499.249.500; C16.320.577.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, decreases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression, affects cotreatment	2
Estradiol	increases expression	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
triphenyl phosphate	affects expression	1
alpha-pinene	increases abundance, affects cotreatment, decreases expression	1
beta-lapachone	decreases expression	1
butyraldehyde	decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
perfluoro-n-nonanoic acid	decreases expression	1
Acrolein	increases abundance, affects cotreatment, decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Ivermectin	decreases expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Rotenone	decreases expression	1
Urethane	increases expression	1
Volatile Organic Compounds	affects cotreatment, decreases expression	1

Cellosaurus cell lines

6 cell lines: 5 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A1CH	HAP1 LARGE (-) POMK (-)	Cancer cell line	Male
CVCL_B3E9	Abcam HEK293T POMK KO	Transformed cell line	Female
CVCL_DX41	HAP1 GNPTAB (-) POMK (-) 1	Cancer cell line	Male
CVCL_DX42	HAP1 GNPTAB (-) POMK (-) 2	Cancer cell line	Male
CVCL_TF18	HAP1 POMK (-) 1	Cancer cell line	Male
CVCL_TF19	HAP1 POMK (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04001595	Not specified	UNKNOWN	Global FKRP Registry
NCT05641103	Not specified	COMPLETED	PREDIGA 2: Spanish Acronym of Educational and Diagnostic Project for Gaucher and ASMD