POMT1

gene
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Also known as LGMD2K

Summary

POMT1 (protein O-mannosyltransferase 1, HGNC:9202) is a protein-coding gene on chromosome 9q34.13, encoding Protein O-mannosyl-transferase 1 (Q9Y6A1). Transfers mannosyl residues to the hydroxyl group of serine or threonine residues.

The protein encoded by this gene is an O-mannosyltransferase that requires interaction with the product of the POMT2 gene for enzymatic function. The encoded protein is found in the membrane of the endoplasmic reticulum. Defects in this gene are a cause of Walker-Warburg syndrome (WWS) and limb-girdle muscular dystrophy type 2K (LGMD2K). Several transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 10585 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): myopathy caused by variation in POMT1 (Definitive, ClinGen) — +8 more curated relationships
  • Clinical variants (ClinVar): 1,307 total — 94 pathogenic, 68 likely-pathogenic
  • Phenotypes (HPO): 201
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_001077365

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9202
Approved symbolPOMT1
Nameprotein O-mannosyltransferase 1
Location9q34.13
Locus typegene with protein product
StatusApproved
AliasesLGMD2K
Ensembl geneENSG00000130714
Ensembl biotypeprotein_coding
OMIM607423
Entrez10585

Gene structure

Transcript identifiers

Ensembl transcripts: 82 — 29 protein_coding, 23 nonsense_mediated_decay, 17 retained_intron, 13 protein_coding_CDS_not_defined

ENST00000341012, ENST00000372220, ENST00000372228, ENST00000402686, ENST00000404875, ENST00000415075, ENST00000418774, ENST00000423007, ENST00000430619, ENST00000441334, ENST00000448212, ENST00000462375, ENST00000467848, ENST00000483472, ENST00000485278, ENST00000494883, ENST00000676640, ENST00000676803, ENST00000676835, ENST00000676915, ENST00000677028, ENST00000677029, ENST00000677099, ENST00000677167, ENST00000677216, ENST00000677221, ENST00000677293, ENST00000677295, ENST00000677444, ENST00000677586, ENST00000677626, ENST00000677677, ENST00000677729, ENST00000677853, ENST00000677944, ENST00000677983, ENST00000678202, ENST00000678264, ENST00000678303, ENST00000678366, ENST00000678546, ENST00000678548, ENST00000678626, ENST00000678693, ENST00000678707, ENST00000678733, ENST00000678739, ENST00000678768, ENST00000678785, ENST00000678795, ENST00000678833, ENST00000678942, ENST00000679023, ENST00000679073, ENST00000679076, ENST00000679111, ENST00000679189, ENST00000679221, ENST00000682070, ENST00000682535, ENST00000682539, ENST00000682563, ENST00000682639, ENST00000682813, ENST00000683110, ENST00000683134, ENST00000683229, ENST00000683231, ENST00000683392, ENST00000683615, ENST00000683712, ENST00000683855, ENST00000683900, ENST00000684062, ENST00000684399, ENST00000684579, ENST00000684679, ENST00000851501, ENST00000851502, ENST00000929070, ENST00000955371, ENST00000955372

RefSeq mRNA: 20 — MANE Select: NM_001077365 NM_001077365, NM_001077366, NM_001136113, NM_001136114, NM_001353193, NM_001353194, NM_001353195, NM_001353196, NM_001353197, NM_001353198, NM_001353199, NM_001353200, NM_001374689, NM_001374690, NM_001374691, NM_001374692, NM_001374693, NM_001374695, NM_001411024, NM_007171

CCDS: CCDS43894, CCDS43895, CCDS48045, CCDS6943, CCDS94516, CCDS94517, CCDS94518, CCDS94519

Canonical transcript exons

ENST00000402686 — 20 exons

ExonStartEnd
ENSE00001288801131511337131511467
ENSE00001426744131509903131509996
ENSE00003462524131520080131520193
ENSE00003495016131522047131522224
ENSE00003537606131519389131519486
ENSE00003561171131509743131509808
ENSE00003572441131518837131518957
ENSE00003579097131515426131515522
ENSE00003587664131506114131506220
ENSE00003609899131508911131509022
ENSE00003633717131506403131506453
ENSE00003638300131512041131512136
ENSE00003651914131518445131518537
ENSE00003667689131521346131521472
ENSE00003786588131507368131507514
ENSE00003787003131513239131513331
ENSE00003788278131510260131510415
ENSE00003899798131502918131503073
ENSE00003903630131522932131523799
ENSE00003906328131504189131504340

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 97.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.4737 / max 151.9426, expressed in 1801 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
9910917.47371801

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489097.12gold quality
cerebellar hemisphereUBERON:000224596.90gold quality
cerebellar cortexUBERON:000212996.67gold quality
left testisUBERON:000453396.61gold quality
right testisUBERON:000453496.46gold quality
cerebellumUBERON:000203794.64gold quality
right uterine tubeUBERON:000130294.05gold quality
testisUBERON:000047393.89gold quality
mucosa of stomachUBERON:000119993.79gold quality
right frontal lobeUBERON:000281093.78gold quality
adenohypophysisUBERON:000219693.75gold quality
cortical plateUBERON:000534393.69gold quality
apex of heartUBERON:000209893.14gold quality
sural nerveUBERON:001548893.01gold quality
lower esophagus muscularis layerUBERON:003583393.01gold quality
lower esophagusUBERON:001347392.98gold quality
right ovaryUBERON:000211892.62gold quality
esophagogastric junction muscularis propriaUBERON:003584192.58gold quality
left ovaryUBERON:000211992.51gold quality
muscle layer of sigmoid colonUBERON:003580592.38gold quality
metanephros cortexUBERON:001053392.24gold quality
anterior cingulate cortexUBERON:000983592.14gold quality
cingulate cortexUBERON:000302792.07gold quality
gastrocnemiusUBERON:000138891.96gold quality
pituitary glandUBERON:000000791.86gold quality
muscle of legUBERON:000138391.80gold quality
stromal cell of endometriumCL:000225591.75gold quality
body of uterusUBERON:000985391.62gold quality
tibial nerveUBERON:000132391.39gold quality
ganglionic eminenceUBERON:000402391.30gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting POMT1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6744-5P99.9366.82748
HSA-MIR-60999.8264.26505
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-120699.3069.321016
HSA-MIR-7160-5P99.1167.172207
HSA-MIR-4711-3P98.9766.871020
HSA-MIR-218-1-3P98.6367.97832
HSA-MIR-6755-3P98.6166.90834
HSA-MIR-429497.8665.721110
HSA-MIR-146B-3P97.8365.29782
HSA-MIR-6859-3P97.2664.69428
HSA-MIR-390796.7665.04662
HSA-MIR-549A-5P96.3568.08587
HSA-MIR-129196.2865.891224
HSA-MIR-3622B-5P94.6264.58835
HSA-MIR-4638-5P92.3165.2386

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 28)

  • Mutations in the O-mannosyltransferase gene POMT1 give rise to the severe neuronal migration disorder Walker-Warburg syndrome (PMID:12369018)
  • Extracellular matrix and nuclear abnormalities in skeletal muscle of a patient with Walker-Warburg syndrome caused by POMT1 mutation. (PMID:12757935)
  • active enzyme complex of POMT1 and POMT2 suggests that the regulation of protein O-mannosylation is complex and appears to be required for normal structure and function of alpha-dystroglycan in muscle and brain (PMID:14699049)
  • The authors report on a patient with Walker-Warburg syndrome and a novel POMT1 mutation. The patient expressed alpha-dystroglycan core protein, but fully glycosylated alpha-DG antibody epitopes were absent, associated with loss of laminin-binding activity (PMID:15037715)
  • Results indicate that mutations in the protein O-mannosyltransferase 1 gene result in a defect of protein O-mannosylation in Walker-Warburg syndrome patients. (PMID:15522202)
  • the phenotype of glycosylation disorders linked to POMT1 mutations. Furthermore, the A200P mutation is part of a conserved core haplotype, indicating an ancestral founder mutation. (PMID:15792865)
  • human protein O-mannosyltransferases 1 and 2 form heterocomplexes which possess protein O-mannosyltransferase activity (PMID:16698797)
  • Several mutations were found in the Protein O-Mannosyltransferase 1 and 2 (POMT1 and POMT2) genes, and one mutation was found in each of the fukutin and fukutin-related protein (FKRP) genes. (PMID:16887026)
  • An inverse Alu-repeated DNA element within exon 3 is associated with Walker Warburg syndrome in French Caucasian families. (PMID:17079174)
  • In conclusion, the lymphoblast-based enzymatic assay is a sensitive and useful method (i) to select patients harbouring POMGNT1, POMT1 or POMT2 mutations; (ii) to assess the pathogenicity of new or already described mutations. (PMID:17869517)
  • Thirteen CMD patients showed mutations in POMT1, But normal brain MRI associated with mental retardation and microcephaly. mutations in POMT1 (six out of 13). (PMID:18513969)
  • We conclude that a significant increase of POMT1 missense mutations may indicate a functional role in neoplastic conditions in individual glioneuronal and glial brain tumors. (PMID:18647264)
  • A double homozygous mutation in the POMT1 gene in two unrelated Gypsy families, is reported. (PMID:19519795)
  • pyramidal neurons frequently displayed abnormal (oblique, horizontal, or inverted) orientation in a 2.5-month-old infant with Walker-Warburg syndrome homozygotic for a novel POMT1 gene mutation (PMID:19639522)
  • the N-glycosylation of POMT1 and POMT2 is required for maintaining the conformation as well as the activity of the POMT1-POMT2 complex. (PMID:19880378)
  • the function of the gene products is only known for POMT1, POMT2, and POMGnT1, all responsible for the O-mannosylglycan biosynthesis (PMID:20816175)
  • the effects of replacing Arg(64), Glu(78) and Arg(138)residues in human POMT1 and POMT2 with Ala on complex formation and enzymatic activity were studied. (PMID:21782786)
  • Three patients with heterozygous POMT1 mutations showed left ventricular (LV) dilation and/or decrease in myocardial contractile force. (PMID:22549409)
  • report of 2 male siblings and an unrelated female with early onset muscular dystrophy and intellectual disability with minimal structural brain anomalies and no ocular abnormalities; a novel missense mutation (c.1958C>T; p.Pro653Leu) was identified (PMID:24491487)
  • Inhibition of POMT1/2 in human mesencyhmal stem cells , resulted in complete abolishment of chondrogenesis and alterations of adipogenic and osteogenic potential together with a lethal effect during myogenic induction. (PMID:26245304)
  • Our results suggest that POMT activity is inversely proportional to clinical severity, and demonstrate that skin fibroblasts can be used for differential diagnosis of patients with alpha-dystroglycanopathies. We have provided clinical, histological, enzymatic and genetic evidence of POMT1 involvement in five unrelated Chinese patients. (PMID:27193224)
  • results demonstrate functional and biochemical similarities between POMT1 and its orthologue from bakers’ yeast Pmt4. (PMID:27358400)
  • These findings may expand phenotype and mutation spectrum of the POMT1 gene. Clinical diagnosis supplemented with molecular screening may result in more accurate diagnoses of, prognoses for, and improved genetic counselling for this disease (PMID:28157257)
  • O-mannosylation of cadherins and protocadherins does not require POMT1 and/or POMT2 in contrast to alpha-dystroglycan, and moreover, the O-Man glycans on cadherins are not elongated. (PMID:28512129)
  • The child was found to carry a heterozygous missense mutation c.1939G>A (p.Ala647Thr) in exon 19 of the protein-O-mannosyltransferase 1 (POMT1) gene inherited from the mother and a heterozygous frameshift mutation c.2141delG (p.Trp714Ter) in exon 20 inherited from the father. (PMID:29419866)
  • In this review, we highlight the present knowledge of the identified disease-associated POMT1 gene mutations and genetic animal models related to the POMT1 gene. (PMID:30454682)
  • Enhanced influenza A H1N1 T cell epitope recognition and cross-reactivity to protein-O-mannosyltransferase 1 in Pandemrix-associated narcolepsy type 1. (PMID:33863907)
  • POMT1 and POMT2 gene mutations result in 2 cases of alpha-dystroglycanopathy.", trans “POMT1POMT22alpha-. (PMID:34565739)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriopomt1ENSDARG00000067670
mus_musculusPomt1ENSMUSG00000039254
rattus_norvegicusPomt1ENSRNOG00000010477
drosophila_melanogasterrtFBGN0003292

Paralogs (3): POMT2 (ENSG00000009830), SDF2L1 (ENSG00000128228), SDF2 (ENSG00000132581)

Protein

Protein identifiers

Protein O-mannosyl-transferase 1Q9Y6A1 (reviewed: Q9Y6A1)

Alternative names: Dolichyl-phosphate-mannose–protein mannosyltransferase 1

All UniProt accessions (35): Q9Y6A1, A0A140VKE0, A0A1V1FTP4, A0A7I2V2G9, A0A7I2V2K0, A0A7I2V2T7, A0A7I2V356, A0A7I2V3H8, A0A7I2V3L5, A0A7I2V445, A0A7I2V4L4, A0A7I2V4U0, A0A7I2V4U3, A0A7I2V505, A0A7I2V524, A0A7I2V568, A0A7I2V5P7, A0A7I2V5S7, A0A7I2V5V4, A0A7I2V5W1, A0A7I2V5X3, A0A7I2YQK3, A0A804HHZ8, A0A804HI97, A0A804HIE5, A0A804HKS2, A0A804HKU5, B4DTW4, B4DWD8, Q5JSZ6, Q5JT02, Q5JT03, Q5JT04, Q5JT05, Q5JT07

UniProt curated annotations — full annotation on UniProt →

Function. Transfers mannosyl residues to the hydroxyl group of serine or threonine residues. Coexpression of both POMT1 and POMT2 is necessary for enzyme activity, expression of either POMT1 or POMT2 alone is insufficient. Essentially dedicated to O-mannosylation of alpha-DAG1 and few other proteins but not of cadherins and protocaherins.

Subunit / interactions. Interacts with POMT2.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed. Highly expressed in testis, heart and pancreas. Detected at lower levels in kidney, skeletal muscle, brain, placenta, lung and liver.

Disease relevance. Muscular dystrophy-dystroglycanopathy congenital with impaired intellectual development B1 (MDDGB1) [MIM:613155] An autosomal recessive disorder characterized by congenital muscular dystrophy associated with intellectual disability and mild structural brain abnormalities. The disease is caused by variants affecting the gene represented in this entry. Muscular dystrophy-dystroglycanopathy congenital with brain and eye anomalies A1 (MDDGA1) [MIM:236670] 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 C1 (MDDGC1) [MIM:609308] An autosomal recessive degenerative myopathy associated with mild intellectual disability without any obvious structural brain abnormality. An abnormal alpha-dystroglycan pattern in observed in the muscle. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Slightly activated by Mg(2+) and inhibited by both Ca(+) and Mn(2+). EDTA ha no effect on activity in vitro.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 39 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q9Y6A1-11yes
Q9Y6A1-22
Q9Y6A1-33
Q9Y6A1-44

RefSeq proteins (20): NP_001070833, NP_001070834, NP_001129585, NP_001129586, NP_001340122, NP_001340123, NP_001340124, NP_001340125, NP_001340126, NP_001340127, NP_001340128, NP_001340129, NP_001361618, NP_001361619, NP_001361620, NP_001361621, NP_001361622, NP_001361624, NP_001397953, NP_009102 (=MANE)

Domains & families (InterPro)

IDNameType
IPR003342ArnT-like_NDomain
IPR016093MIR_motifDomain
IPR027005PMT-likeFamily
IPR032421PMT_4TMCDomain
IPR036300MIR_dom_sfHomologous_superfamily

Pfam: PF02366, PF02815, PF16192

Enzyme classification (BRENDA):

  • EC 2.4.1.109 — dolichyl-phosphate-mannose-protein mannosyltransferase (BRENDA: 24 organisms, 130 substrates, 16 inhibitors, 22 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

13 substrates with measured Km, best-characterized 13. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
SYNTHETIC PEPTIDE BASED ON A MUCIN-LIKE DOMAIN I0.63–9.75
AC-TYR-ALA-THR-ALA-VAL-NH20.25–153
RSPSPSTQ10–202
TYR-ASN-PRO-THR-SER-VAL1–3.32
AC-ALA-THR-ALA-NH26.71
AC-TYR-ASN-PRO-THR-SER-VAL-NH24.31
BIOTIN-TYR-LEU-ALA-VAL-NH20.11
BIOTIN-TYR-PRO-THR-ALA-VAL-NH20.851
BIOTIN-TYR-THR-ALA-VAL-NH20.0751
DOLICHYL PHOSPHATE D-MANNOSE0.41
TYR-ALA-THR-ALA-VAL2.21
TYR-LEU-THR-ALA-VAL2.51
TYR-PRO-THR-ALA-VAL7.31

Catalyzed reactions (Rhea), 2 shown:

  • a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate + L-seryl-[protein] = 3-O-(alpha-D-mannosyl)-L-seryl-[protein] + a di-trans,poly-cis-dolichyl phosphate + H(+) (RHEA:17377)
  • a di-trans,poly-cis-dolichyl beta-D-mannosyl phosphate + L-threonyl-[protein] = 3-O-(alpha-D-mannosyl)-L-threonyl-[protein] + a di-trans,poly-cis-dolichyl phosphate + H(+) (RHEA:53396)

UniProt features (49 total): sequence variant 19, transmembrane region 12, sequence conflict 8, domain 3, glycosylation site 3, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y6A1-F188.090.67

Functional residue map

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

Glycosylation sites (3): 435, 471, 539

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-5083629Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2
R-HSA-5083633Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1
R-HSA-8932504DAG1 core M2 glycosylations
R-HSA-8932505DAG1 core M3 glycosylations
R-HSA-8932506DAG1 core M1 glycosylations
R-HSA-9768727Regulation of CDH1 posttranslational processing and trafficking to plasma membrane

MSigDB gene sets: 410 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, GOCC_SECRETORY_GRANULE, CMYB_01, CHANDRAN_METASTASIS_DN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP, XU_GH1_AUTOCRINE_TARGETS_DN, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, CHANDRAN_METASTASIS_TOP50_DN, GOCC_SECRETORY_VESICLE, GOCC_TRANSFERASE_COMPLEX, GOCC_MEMBRANE_PROTEIN_COMPLEX

GO Biological Process (4): protein O-linked glycosylation (GO:0006493), extracellular matrix organization (GO:0030198), protein O-linked glycosylation via mannose (GO:0035269), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (6): mannosyltransferase activity (GO:0000030), dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169), metal ion binding (GO:0046872), protein binding (GO:0005515), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757)

GO Cellular Component (7): acrosomal vesicle (GO:0001669), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), sarcoplasmic reticulum (GO:0016529), dolichyl-phosphate-mannose-protein mannosyltransferase complex (GO:0031502), endomembrane system (GO:0012505)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
DAG1 glycosylations3
Diseases associated with O-glycosylation of proteins2
Regulation of CDH1 Expression and Function1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
glycoprotein biosynthetic process1
extracellular structure organization1
external encapsulating structure organization1
protein O-linked glycosylation1
hexosyltransferase activity1
mannosyltransferase activity1
protein O-linked glycosylation via mannose1
catalytic activity, acting on a protein1
cation binding1
binding1
catalytic activity1
transferase activity1
secretory granule1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
endoplasmic reticulum1
sarcoplasm1
endoplasmic reticulum membrane1
mannosyltransferase complex1
membrane protein complex1
endoplasmic reticulum protein-containing complex1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1338 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POMT1FKTNO75072986
POMT1FKRPQ9H9S5986
POMT1POMGNT1Q8WZA1986
POMT1DAG1Q14118978
POMT1POMT2Q9UKY4966
POMT1LARGE1O95461875
POMT1POMGNT2Q8NAT1874
POMT1RXYLT1Q9Y2B1858
POMT1B3GALNT2Q8NCR0855
POMT1POMKQ9H5K3847
POMT1LAMA2P24043809
POMT1DPM3Q9P2X0805
POMT1B4GAT1O43505802
POMT1GMPPBQ9Y5P6796
POMT1AGRNO00468795

IntAct

45 interactions, top by confidence:

ABTypeScore
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
VWCEZNF316psi-mi:“MI:0914”(association)0.530
PCDHB7C2CD2Lpsi-mi:“MI:0914”(association)0.530
B4GAT1ADCY6psi-mi:“MI:0914”(association)0.530
TMPRSS12FZD6psi-mi:“MI:0914”(association)0.530
GABRA3HLA-Cpsi-mi:“MI:0914”(association)0.530
POMT1POMT2psi-mi:“MI:0915”(physical association)0.460
POMT1POMT2psi-mi:“MI:0403”(colocalization)0.460
DENND11psi-mi:“MI:0914”(association)0.350
MDENND11psi-mi:“MI:0914”(association)0.350
CANXHLA-Apsi-mi:“MI:0914”(association)0.350
NSDHLATP2A2psi-mi:“MI:0914”(association)0.350
PCDHA4TMEM223psi-mi:“MI:0914”(association)0.350
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
CHRNA4TMEM223psi-mi:“MI:0914”(association)0.350
PCDHA8TMEM223psi-mi:“MI:0914”(association)0.350
CLEC12BGXYLT2psi-mi:“MI:0914”(association)0.350
ZDHHC12NBASpsi-mi:“MI:0914”(association)0.350
MPPE1FAM234Bpsi-mi:“MI:0914”(association)0.350
TCTN2TMEM131Lpsi-mi:“MI:0914”(association)0.350
CHRNB2TMEM131Lpsi-mi:“MI:0914”(association)0.350
PCDHB6KLRG2psi-mi:“MI:0914”(association)0.350
ST14LIPT2psi-mi:“MI:0914”(association)0.350
RFTN2RABGAP1Lpsi-mi:“MI:0914”(association)0.350
HTR3CGET1psi-mi:“MI:0914”(association)0.350
SLC3A2GET1psi-mi:“MI:0914”(association)0.350
HFEPODXLpsi-mi:“MI:0914”(association)0.350
HPNTOR1Apsi-mi:“MI:0914”(association)0.350
CD1EADAM10psi-mi:“MI:0914”(association)0.350
APOC3EMC8psi-mi:“MI:0914”(association)0.350

BioGRID (92): POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS), POMT1 (Affinity Capture-MS)

ESM2 similar proteins: A0A8C2M425, A1L1J9, B0BNG2, O60725, O75908, O77759, O88269, O88908, O95255, Q0P4J9, Q290J8, Q3T1L5, Q3TAE8, Q3UV71, Q499P8, Q49LS7, Q4R4E1, Q4VV71, Q5F380, Q5KR61, Q5R8F6, Q5RAH7, Q5RKL5, Q6AZ83, Q6NVG1, Q7SXZ1, Q7T310, Q7TPN3, Q7TQM4, Q86VD9, Q8AVI9, Q8BTP0, Q8C0T0, Q8C3X8, Q8CI59, Q8IUR5, Q8K2A8, Q8L638, Q8R1J1, Q8R4P9

Diamond homologs: F1Q8R9, F1QF89, O13898, O74189, P31382, P33775, P42934, P46971, P47190, P52867, Q29IL2, Q2LZ62, Q3SZ45, Q54P23, Q59X23, Q5A688, Q5ACU3, Q5ADM9, Q8BGQ4, Q8R2R1, Q93ZE8, Q99470, Q99PR0, Q9C100, Q9DCT5, Q9UKY4, Q9VTK2, Q9W5D4, Q9Y6A1, O42933, Q9ESP1, Q3T083, Q9HCN8, A0R3E8, L8F4Z2

SIGNOR signaling

1 interactions.

AEffectBMechanism
POMT1“form complex”POMTbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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.

GO biological processes:

GO termPartnersFoldFDR
monoatomic ion transmembrane transport619.5×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

1307 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic94
Likely pathogenic68
Uncertain significance426
Likely benign466
Benign72

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1067618NM_001077365.2(POMT1):c.427+1G>APathogenic
1075349NM_001077365.2(POMT1):c.1204dup (p.His402fs)Pathogenic
1076965NM_001077365.2(POMT1):c.160_161insTTTTTTTTTTTTTTTNNNNNNNNNNTCACCGTTTTAGCCGGGATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCAGTACATCTCTTTTT (p.Tyr54delinsPhePhePhePhePheXaaXaaXaaXaaHisArgPheSerArgAspGlyLeuAspLeuLeuThrSerTer)Pathogenic
1120088NM_001077365.2(POMT1):c.1255C>T (p.Gln419Ter)Pathogenic
1192212NM_001077365.2(POMT1):c.1272+1G>APathogenic
1252077NM_001077365.2(POMT1):c.1175+3delPathogenic
1323488NM_001077365.2(POMT1):c.1158del (p.Thr387fs)Pathogenic
1323489NM_001077365.2(POMT1):c.633C>G (p.Tyr211Ter)Pathogenic
1359283NM_001077365.2(POMT1):c.859_871del (p.Gly287fs)Pathogenic
1364191NM_001077365.2(POMT1):c.58dup (p.Val20fs)Pathogenic
1451349NM_001077365.2(POMT1):c.72del (p.Met25fs)Pathogenic
1470886NM_001077365.2(POMT1):c.605+1G>TPathogenic
1516923NC_000009.11:g.(?134389752)(134390863_?)delPathogenic
162594NM_001077365.2(POMT1):c.1478dup (p.Tyr493Ter)Pathogenic
1696829NM_001077365.2(POMT1):c.1417G>C (p.Gly473Arg)Pathogenic
1696831NM_001077365.2(POMT1):c.1093_1094insGGAGCACGGTGTGGAACGTGGG (p.Val365fs)Pathogenic
1930280NM_001077365.2(POMT1):c.720del (p.Leu240fs)Pathogenic
194859NM_001077365.2(POMT1):c.1798C>T (p.Arg600Ter)Pathogenic
1997263NM_001077365.2(POMT1):c.1061G>A (p.Trp354Ter)Pathogenic
1998900NM_001077365.2(POMT1):c.529C>T (p.Gln177Ter)Pathogenic
1998907NM_001077365.2(POMT1):c.2141G>A (p.Trp714Ter)Pathogenic
2020409NM_001077365.2(POMT1):c.145del (p.Gln49fs)Pathogenic
2062446NM_001077365.2(POMT1):c.2113_2119del (p.Ser705fs)Pathogenic
212739NM_001077365.2(POMT1):c.558G>A (p.Trp186Ter)Pathogenic
2229059NM_001077365.2(POMT1):c.633C>A (p.Tyr211Ter)Pathogenic
2413915NM_001077365.2(POMT1):c.385del (p.Ser129fs)Pathogenic
2677995NM_001077365.2(POMT1):c.291del (p.Ser97fs)Pathogenic
2678001NM_001077365.2(POMT1):c.1477_1486del (p.Tyr493fs)Pathogenic
2678012NM_001077365.2(POMT1):c.2142del (p.Arg713_Trp714insTer)Pathogenic
280761NM_001077365.2(POMT1):c.2113_2114dup (p.Pro706fs)Pathogenic

SpliceAI

3694 predictions. Top by Δscore:

VariantEffectΔscore
9:131503119:G:Tdonor_gain1.0000
9:131504336:GTGGT:Gdonor_gain1.0000
9:131504339:GT:Gdonor_gain1.0000
9:131504341:G:GGdonor_gain1.0000
9:131504346:C:Gdonor_gain1.0000
9:131506236:A:Tdonor_gain1.0000
9:131506401:A:AGacceptor_gain1.0000
9:131506401:A:ATacceptor_loss1.0000
9:131506401:AG:Aacceptor_gain1.0000
9:131506402:G:GAacceptor_gain1.0000
9:131506402:GG:Gacceptor_gain1.0000
9:131506402:GGTT:Gacceptor_gain1.0000
9:131506638:A:Tdonor_gain1.0000
9:131508903:T:TAacceptor_gain1.0000
9:131508908:CA:Cacceptor_loss1.0000
9:131508909:A:AGacceptor_gain1.0000
9:131508909:A:ATacceptor_loss1.0000
9:131508910:G:GGacceptor_gain1.0000
9:131508910:GA:Gacceptor_gain1.0000
9:131508910:GAGA:Gacceptor_gain1.0000
9:131508910:GAGAA:Gacceptor_gain1.0000
9:131509018:CACAG:Cdonor_loss1.0000
9:131509019:ACAGG:Adonor_loss1.0000
9:131509021:AGGTA:Adonor_loss1.0000
9:131509024:T:Gdonor_loss1.0000
9:131510258:A:Cacceptor_loss1.0000
9:131510259:GGTCT:Gacceptor_gain1.0000
9:131510413:GAG:Gdonor_gain1.0000
9:131510414:AGGTA:Adonor_loss1.0000
9:131510416:G:GGdonor_gain1.0000

AlphaMissense

4715 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:131506115:T:CF42L0.998
9:131506117:T:AF42L0.998
9:131506117:T:GF42L0.998
9:131511388:T:CS325P0.998
9:131512086:T:GC366W0.998
9:131512110:C:AN374K0.998
9:131512110:C:GN374K0.998
9:131512114:T:AW376R0.998
9:131512114:T:CW376R0.998
9:131515474:C:GC430W0.998
9:131515514:T:AW444R0.998
9:131515514:T:CW444R0.998
9:131511439:C:GH342D0.997
9:131512116:G:CW376C0.997
9:131512116:G:TW376C0.997
9:131518478:T:AW458R0.997
9:131518478:T:CW458R0.997
9:131518927:T:AW508R0.997
9:131518927:T:CW508R0.997
9:131522139:T:CF662L0.997
9:131522141:C:AF662L0.997
9:131522141:C:GF662L0.997
9:131511395:T:AV327D0.996
9:131511437:T:AL341H0.996
9:131511442:T:CS343P0.996
9:131511443:C:TS343F0.996
9:131515516:G:CW444C0.996
9:131515516:G:TW444C0.996
9:131521369:C:AN596K0.996
9:131521369:C:GN596K0.996

dbSNP variants (sampled 300 via entrez): RS1000022900 (9:131514228 G>A), RS1000035954 (9:131504799 G>C), RS1000174991 (9:131519509 TG>T), RS1000176985 (9:131510973 G>A,C), RS1000296937 (9:131516224 C>G,T), RS1000395946 (9:131521032 G>A), RS1000404385 (9:131520777 C>T), RS1001093763 (9:131502629 T>A,G), RS1001441814 (9:131506312 C>A,G), RS1001483698 (9:131505714 C>G), RS1001616712 (9:131514814 G>C,T), RS1001706684 (9:131516607 G>A), RS1001748795 (9:131516900 C>T), RS1001900403 (9:131521616 T>C,G), RS1002499531 (9:131515061 C>T)

Disease associations

OMIM: gene MIM:607423 | disease phenotypes: MIM:236670, MIM:609308, MIM:613155, MIM:253600, MIM:616094

GenCC curated gene-disease

DiseaseClassificationInheritance
muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1DefinitiveAutosomal recessive
muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1StrongAutosomal recessive
myopathy caused by variation in POMT1StrongAutosomal recessive
congenital muscular dystrophy with cerebellar involvementSupportiveAutosomal recessive
congenital muscular dystrophy with intellectual disabilitySupportiveAutosomal recessive
congenital muscular dystrophy without intellectual disabilitySupportiveAutosomal recessive
muscle-eye-brain diseaseSupportiveAutosomal recessive
autosomal recessive limb-girdle muscular dystrophy type 2KSupportiveAutosomal recessive
muscular dystrophy-dystroglycanopathy, type ASupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
myopathy caused by variation in POMT1DefinitiveAR

Mondo (19): muscular dystrophy-dystroglycanopathy, type A (MONDO:0000171), autosomal recessive limb-girdle muscular dystrophy type 2K (MONDO:0012248), muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 (MONDO:0013159), muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 (MONDO:0009364), autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152), congenital muscular dystrophy (MONDO:0019950), pyridoxine-dependent epilepsy (MONDO:0009945), congenital nervous system disorder (MONDO:0002320), muscular dystrophy-dystroglycanopathy, type C (MONDO:0000173), cerebellar ataxia (MONDO:0000437), sensory peripheral neuropathy (MONDO:0002321), hearing loss disorder (MONDO:0005365), myopathy caused by variation in POMT1 (MONDO:0700070), limb-girdle muscular dystrophy due to POMK deficiency (MONDO:0014489), intellectual disability (MONDO:0001071)

Orphanet (9): POMT1-related limb-girdle muscular dystrophy R11 (Orphanet:86812), Walker-Warburg syndrome (Orphanet:899), Muscle-eye-brain disease (Orphanet:588), Autosomal recessive limb-girdle muscular dystrophy (Orphanet:102015), Congenital muscular dystrophy (Orphanet:97242), Pyridoxine-dependent-developmental and epileptic encephalopathy (Orphanet:3006), Rare ataxia (Orphanet:102002), Limb-girdle muscular dystrophy due to POMK deficiency (Orphanet:445110), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

201 total (30 of 201 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000050Hypoplastic male external genitalia
HP:0000054Micropenis
HP:0000110Renal dysplasia
HP:0000158Macroglossia
HP:0000175Cleft palate
HP:0000176Submucous cleft hard palate
HP:0000193Bifid uvula
HP:0000204Cleft upper lip
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000256Macrocephaly
HP:0000298Mask-like facies
HP:0000340Sloping forehead
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000369Low-set ears
HP:0000411Protruding ear
HP:0000413Atresia of the external auditory canal
HP:0000478Abnormality of the eye
HP:0000482Microcornea
HP:0000485Megalocornea
HP:0000486Strabismus
HP:0000501Glaucoma
HP:0000505Visual impairment
HP:0000518Cataract
HP:0000519Developmental cataract
HP:0000525Abnormality iris morphology
HP:0000528Anophthalmia

GWAS associations

0 associations (top):

MeSH disease descriptors (6)

DescriptorNameTree numbers
D002524Cerebellar AtaxiaC10.228.140.252.190; C10.597.350.090.500; C23.888.592.350.090.200
D034381Hearing LossC09.218.458.341; C10.597.751.418.341; C23.888.592.763.393.341
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D058494Walker-Warburg SyndromeC10.500.507.450.499.249.500; C11.270.881; C16.131.666.507.450.499.249.500; C16.320.577.750
C538640Limb-girdle muscular dystrophy autosomal recessive (supp.)
C536254Pyridoxine-dependent epilepsy (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
methacrylaldehydeincreases oxidation, increases abundance, affects cotreatment, decreases expression2
Acroleinaffects cotreatment, decreases expression, increases oxidation, increases abundance2
Ozoneaffects cotreatment, decreases expression, increases oxidation, increases abundance2
alpha-pineneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
beta-lapachoneincreases expression1
sodium arseniteaffects cotreatment, decreases expression, increases abundance1
manganese chlorideaffects cotreatment, decreases expression, increases abundance1
beta-methylcholineaffects expression1
CGP 52608affects binding, increases reaction1
Temozolomideincreases expression1
Arsenic Trioxidedecreases expression1
Air Pollutantsincreases abundance, increases oxidation, affects cotreatment, decreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance1
Benzo(a)pyreneincreases methylation1
Dactinomycinincreases expression1
Manganeseaffects cotreatment, decreases expression, increases abundance1
Smokedecreases expression1
Valproic Aciddecreases expression1
Vanadatesdecreases expression1
Antirheumatic Agentsincreases expression1
Copper Sulfatedecreases expression1
Volatile Organic Compoundsaffects cotreatment, decreases expression, increases oxidation1

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 finite cell line

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

CellosaurusNameCategorySex
CVCL_E2H7HAP1 POMT1 (-) 3Cancer cell lineMale
CVCL_E2H8HAP1 POMT1 (-) 4Cancer cell lineMale
CVCL_JF24GM23363Finite cell lineFemale
CVCL_TF20HAP1 POMT1 (-) 1Cancer cell lineMale
CVCL_TF21HAP1 POMT1 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01422200PHASE4COMPLETEDFlu Vaccine Study in Neuromuscular Patients 2011
NCT00950196PHASE4COMPLETEDAmantadine for Improving Neurologic Symptoms in Ataxia-Telangiectasia
NCT04107740PHASE4COMPLETEDC-Trelin Orally Disintegrated(OD) Tablet 5mg in Ataxia Due to Spinocerebellar Degeneration
NCT00205881PHASE4COMPLETEDBilateral Benefit in Adult Users of the HiRes 90K Bionic Ear System
NCT00331539PHASE4UNKNOWNRelationship Between Auto NRT and Behavioural T & C Levels With the Nucleus Freedom Cochlear Implant
NCT00424307PHASE4UNKNOWNBilateral Cochlear Implant Benefit in Young Children
NCT00765635PHASE4COMPLETEDChlorobutanol, Potassium Carbonate, and Irrigation in Cerumen Removal
NCT03321006PHASE4COMPLETEDTreating Hearing Loss to Improve Mood and Cognition in Older Adults
NCT01970098PHASE3COMPLETEDA Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970111PHASE3COMPLETEDAn Extension Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970124PHASE3COMPLETEDA Long-Term Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970137PHASE3COMPLETEDA 24-week Open-label Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT02889302PHASE3COMPLETEDAn Additional Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT03408080PHASE3ACTIVE_NOT_RECRUITINGOpen Pilot Trial of BHV-4157
NCT03701399PHASE3ACTIVE_NOT_RECRUITINGTroriluzole in Adult Participants With Spinocerebellar Ataxia
NCT03901638PHASE3TERMINATEDTllsh2910 for Ataxia and Gut Microbiota Alteration in Patients of Multiple System Atrophy
NCT07040137PHASE3RECRUITINGConfirmatory Study 3 of KPS-0373 in Patients With Spinocerebellar Degeneration
NCT01526564PHASE3COMPLETEDClinical Study on Acetyl-L-Carnitine
NCT01499901PHASE3WITHDRAWNComparison of the Bilateral Sequential and Simultaneous Cochlear Implantation in the Deaf Children
NCT02561091PHASE3COMPLETEDAM-111 in the Treatment of Acute Inner Ear Hearing Loss
NCT03331627PHASE3COMPLETEDSafety and Efficacy of STR001-IT and STR001-ER in Patients With SSHL
NCT05532657PHASE3ACTIVE_NOT_RECRUITINGACHIEVE Brain Health Follow-Up Study
NCT00034242PHASE2COMPLETEDHigh-Dose Intravenous Immunoglobulin to Treat Cerebellar Degeneration
NCT00202397PHASE2COMPLETEDEffect of Riluzole as a Symptomatic Approach in Patients With Chronic Cerebellar Ataxia
NCT00863538PHASE2COMPLETEDPhase II Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01004016PHASE2COMPLETEDA Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01350440PHASE2COMPLETEDSafety and Efficacy of Intravenous Immune Globulin in Treating Spinocerebellar Ataxia
NCT02540655PHASE2COMPLETEDEfficacy and Safety Study of Stemchymal® in Polyglutamine Spinocerebellar Ataxia
NCT03932669PHASE2COMPLETEDEffect of Nilotinib in Cerebellar Ataxia Patients
NCT04301284PHASE2WITHDRAWNStudy of CAD-1883 for Spinocerebellar Ataxia
NCT05125666PHASE2UNKNOWNEfficacy of Dual Task Training on Children With Ataxia After Medulloblastoma Resection
NCT06397274PHASE2NOT_YET_RECRUITINGStemchymal® for Polyglutamine Spinocerebellar Ataxia
NCT00013455PHASE2COMPLETEDQuantifying Auditory Perceptual Learning Following Hearing Aid Fitting
NCT00323427PHASE2COMPLETEDClinical Trial of the Living Well With Hearing Loss Workshop
NCT00552786PHASE2COMPLETEDAntioxidation Medication for Noise-induced Hearing Loss
NCT00802425PHASE2COMPLETEDEfficacy of AM-111 in Patients With Acute Sensorineural Hearing Loss
NCT01139281PHASE2COMPLETEDThe Protective Effect of Ginkgo Biloba Extract on Cisplatin-induced Ototoxicity in Humans
NCT01451853PHASE2UNKNOWNSPI-1005 for Prevention and Treatment of Chemotherapy Induced Hearing Loss
NCT01588925PHASE2COMPLETEDHearing Preservation Using Dexamethasone and Hyaluronic Acid for Cochlear Implantation
NCT01773278PHASE2RECRUITINGCholesterol and Antioxidant Treatment in Patients With Smith-Lemli-Opitz Syndrome (SLOS)