Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	10585
Gene name Gene Name - the full gene name approved by the HGNC.	Protein O-mannosyltransferase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	POMT1
Synonyms (NCBI Gene) Gene synonyms aliases	LGMD2K, LGMDR11, MDDGA1, MDDGB1, MDDGC1, RT
Chromosome Chromosome number	9
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	9q34.13
Summary Summary of gene provided in NCBI Entrez Gene.	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 o

Show/Hide all(66)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28941782	G>A	Pathogenic	Intron variant, missense variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant
rs119462981	C>T	Pathogenic	Non coding transcript variant, 5 prime UTR variant, stop gained, coding sequence variant, missense variant
rs119462982	G>C	Pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs119462983	G>A	Pathogenic	Non coding transcript variant, 5 prime UTR variant, intron variant, coding sequence variant, missense variant
rs119462986	G>A,C	Pathogenic	Coding sequence variant, non coding transcript variant, synonymous variant, missense variant
rs119462987	G>A	Pathogenic-likely-pathogenic, likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs138064523	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Non coding transcript variant, synonymous variant, 5 prime UTR variant, intron variant, coding sequence variant
rs138902646	C>A,T	Conflicting-interpretations-of-pathogenicity, pathogenic-likely-pathogenic, likely-benign, uncertain-significance	Coding sequence variant, non coding transcript variant, synonymous variant, stop gained
rs140553130	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, non coding transcript variant, synonymous variant
rs147143094	G>A,C	Conflicting-interpretations-of-pathogenicity	Terminator codon variant, synonymous variant, non coding transcript variant, stop lost
rs148887050	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, 5 prime UTR variant, stop gained, synonymous variant, non coding transcript variant, coding sequence variant
rs149682171	C>T	Likely-pathogenic, pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs150937126	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	5 prime UTR variant, intron variant, synonymous variant, non coding transcript variant, coding sequence variant
rs200056620	C>G,T	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, stop gained, missense variant, 5 prime UTR variant
rs200465419	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, non coding transcript variant, synonymous variant, coding sequence variant, 5 prime UTR variant
rs201533471	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, 5 prime UTR variant, coding sequence variant, intron variant, non coding transcript variant
rs202095070	A>G	Benign-likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs202121299	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, intron variant, non coding transcript variant, coding sequence variant
rs368975092	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs371653610	C>A,G,T	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs376373313	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs397514501	A>G	Pathogenic	5 prime UTR variant, missense variant, coding sequence variant, intron variant, non coding transcript variant
rs397515400	C>T	Pathogenic	Intron variant, non coding transcript variant, missense variant, coding sequence variant
rs398124243	AG>TC	Likely-pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs398124244	A>C,G	Likely-pathogenic	Synonymous variant, 5 prime UTR variant, missense variant, coding sequence variant, intron variant, non coding transcript variant
rs398124245	->G	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs398124247	C>G,T	Pathogenic	5 prime UTR variant, stop gained, missense variant, coding sequence variant, non coding transcript variant
rs587777817	->G	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs587777818	CCT>-	Pathogenic	Non coding transcript variant, coding sequence variant, inframe deletion
rs587777819	TC>-,TCTC	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs587777820	ATG>-	Pathogenic	5 prime UTR variant, non coding transcript variant, inframe deletion, coding sequence variant, intron variant
rs745738628	G>C	Pathogenic	Splice acceptor variant
rs746823238	G>T	Pathogenic	Splice donor variant, intron variant
rs750195040	CTT>-	Likely-pathogenic, pathogenic	Inframe deletion, intron variant, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs750453909	AAGA>-,AAGAAAGA	Pathogenic, likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs756973046	C>T	Pathogenic	Intron variant, stop gained, 5 prime UTR variant, coding sequence variant, non coding transcript variant
rs761848742	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs765230689	T>A,C	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, stop gained, 5 prime UTR variant, synonymous variant
rs766648827	G>C,T	Pathogenic	Splice donor variant
rs772370177	G>A,T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, stop gained, 5 prime UTR variant, missense variant
rs772980661	G>A,C	Likely-pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, synonymous variant, missense variant
rs776061161	G>A,T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant, splice donor variant, 5 prime UTR variant, intron variant
rs776988725	T>C,G	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs777437871	C>T	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs778418119	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs794727208	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs886041907	->T	Pathogenic	Splice donor variant, intron variant
rs886043307	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant, 5 prime UTR variant, stop gained
rs886043948	C>A,T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs1032439203	AG>-	Pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1051679985	G>A	Pathogenic	Splice donor variant, intron variant
rs1057520142	GGT>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, splice acceptor variant
rs1250351189	T>-	Likely-pathogenic	Intron variant, 5 prime UTR variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1315540509	->CGCTGGGTGCTGGCTG	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1356791510	A>-	Pathogenic	5 prime UTR variant, non coding transcript variant, frameshift variant, intron variant, coding sequence variant
rs1453773610	A>C,T	Likely-pathogenic	Intron variant, splice acceptor variant
rs1554773448	A>G	Likely-pathogenic	5 prime UTR variant, splice acceptor variant, intron variant
rs1554773974	CT>-	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, frameshift variant
rs1554778005	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1564341846	C>A	Pathogenic	Intron variant, 5 prime UTR variant, missense variant, coding sequence variant, non coding transcript variant
rs1564364615	CT>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1564365317	T>C	Likely-pathogenic	Splice donor variant
rs1588375386	C>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant, non coding transcript variant
rs1588377489	G>-	Likely-pathogenic	Coding sequence variant, splice donor variant, 5 prime UTR variant, intron variant, non coding transcript variant, frameshift variant
rs1588391612	C>A	Pathogenic	Stop gained, coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs1588409344	AGTG>-	Pathogenic	Intron variant, splice donor variant

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miRTarBase ID	miRNA	Experiments
MIRT1250058	hsa-miR-103a	CLIP-seq
MIRT1250059	hsa-miR-107	CLIP-seq
MIRT1250060	hsa-miR-1184	CLIP-seq
MIRT1250061	hsa-miR-3620	CLIP-seq
MIRT1250062	hsa-miR-451b	CLIP-seq
MIRT1250063	hsa-miR-4766-3p	CLIP-seq
MIRT2073812	hsa-miR-1291	CLIP-seq
MIRT2073813	hsa-miR-2467-5p	CLIP-seq
MIRT2073814	hsa-miR-3151	CLIP-seq
MIRT2073815	hsa-miR-3188	CLIP-seq
MIRT2073816	hsa-miR-328	CLIP-seq
MIRT1250061	hsa-miR-3620	CLIP-seq
MIRT2073817	hsa-miR-3975	CLIP-seq
MIRT2073818	hsa-miR-4527	CLIP-seq
MIRT2073819	hsa-miR-4649-3p	CLIP-seq
MIRT2073820	hsa-miR-4663	CLIP-seq
MIRT2073821	hsa-miR-485-5p	CLIP-seq
MIRT2073822	hsa-miR-767-3p	CLIP-seq
MIRT2300652	hsa-miR-1228	CLIP-seq
MIRT2300653	hsa-miR-3157-5p	CLIP-seq
MIRT2300654	hsa-miR-329	CLIP-seq
MIRT2300655	hsa-miR-362-3p	CLIP-seq
MIRT2300656	hsa-miR-4264	CLIP-seq
MIRT2300657	hsa-miR-4691-3p	CLIP-seq
MIRT2300658	hsa-miR-4699-5p	CLIP-seq
MIRT2300659	hsa-miR-4797-3p	CLIP-seq
MIRT2300660	hsa-miR-512-5p	CLIP-seq
MIRT2300661	hsa-miR-642b	CLIP-seq
MIRT2300652	hsa-miR-1228	CLIP-seq
MIRT2300654	hsa-miR-329	CLIP-seq
MIRT2300655	hsa-miR-362-3p	CLIP-seq
MIRT2300658	hsa-miR-4699-5p	CLIP-seq
MIRT2300661	hsa-miR-642b	CLIP-seq
MIRT2300652	hsa-miR-1228	CLIP-seq
MIRT2688368	hsa-miR-1289	CLIP-seq
MIRT2300653	hsa-miR-3157-5p	CLIP-seq
MIRT2688369	hsa-miR-3198	CLIP-seq
MIRT2300654	hsa-miR-329	CLIP-seq
MIRT2300655	hsa-miR-362-3p	CLIP-seq
MIRT2688370	hsa-miR-3692	CLIP-seq
MIRT2688371	hsa-miR-4257	CLIP-seq
MIRT2300656	hsa-miR-4264	CLIP-seq
MIRT2688372	hsa-miR-4294	CLIP-seq
MIRT2688373	hsa-miR-4309	CLIP-seq
MIRT2688374	hsa-miR-4330	CLIP-seq
MIRT2300657	hsa-miR-4691-3p	CLIP-seq
MIRT2300658	hsa-miR-4699-5p	CLIP-seq
MIRT2688375	hsa-miR-4728-5p	CLIP-seq
MIRT2300659	hsa-miR-4797-3p	CLIP-seq
MIRT2300660	hsa-miR-512-5p	CLIP-seq
MIRT2300661	hsa-miR-642b	CLIP-seq

Show/Hide all(26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000030	Function	Mannosyltransferase activity	IEA
GO:0000030	Function	Mannosyltransferase activity	IMP	28512129
GO:0000030	Function	Mannosyltransferase activity	TAS	10366449
GO:0001669	Component	Acrosomal vesicle	IEA
GO:0004169	Function	Dolichyl-phosphate-mannose-protein mannosyltransferase activity	IBA
GO:0004169	Function	Dolichyl-phosphate-mannose-protein mannosyltransferase activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005783	Component	Endoplasmic reticulum	TAS	10366449
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	14699049
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006486	Process	Protein glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	IEA
GO:0006493	Process	Protein O-linked glycosylation	TAS	10366449
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	10366449
GO:0016529	Component	Sarcoplasmic reticulum	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0030198	Process	Extracellular matrix organization	IEA
GO:0031502	Component	Dolichyl-phosphate-mannose-protein mannosyltransferase complex	IEA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IBA
GO:0035269	Process	Protein O-linked glycosylation via mannose	IMP	28512129
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
607423	9202	ENSG00000130714

Protein

UniProt ID

Q9Y6A1

Protein name

Protein O-mannosyl-transferase 1 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransferase 1)

Protein 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 (PubMed:12369018, PubMed:14699049

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02366	PMT	20 → 289	Dolichyl-phosphate-mannose-protein mannosyltransferase	Family
PF02815	MIR	332 → 500	MIR domain	Domain
PF16192	PMT_4TMC	542 → 740	C-terminal four TMM region of protein-O-mannosyltransferase	Family

Tissue specificity

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

Sequence

MWGFLKRPVVVTADINLSLVALTGMGLLSRLWRLTYPRAVVFDEVYYGQYISFYMKQIFF
LDDSGPPFGHMVLALGGYLGGFDGNFLWNRIGAEYSSNVPVWSLRLLPALAGALSVPMAY
QIVLELHFSHCAAMGAALLMLIENALITQSRLMLLESVLIFFNLLAVLSYLKFFNCQKHS
PFSLSWWFWLTLTGVACSCAVGIKYMGVFTYVLVLGVAAVHAWHLLGDQTLSNVGADVQC
CMRPACMGQMQMSQGVCVFCHLLARAVALLVIPVVLYLLFFYVHLILVFRSGPHDQIMSS
AFQASLEGGLARITQGQPLEVAFGSQVTLRNVFGKPVPCWLHSHQDTYPMIYENGRGSSH
QQQVTCYPFKDVNNWWIVKDPRRHQLVVSSPPRPVRHGDMVQLVHGMTTRSLNTHDVAAP
LSPHSQEVSCYIDYNISMPAQNLWRLEIVNRGSDTDVWKTILSEVRFVHVNTSAVLKLSG
AHLPDWGYRQLEIVGEKLSRGYHGSTVWNVEEHRYGASQEQRERERELHSPAQVDVSRNL
SFMARFSELQWRMLALRSDDSEHKYSSSPLEWVTLDTNIAYWLHPRTSAQIHLLGNIVIW
VSGSLALAIYALLSLWYLLRRRRNVHDLPQDAWLRWVLAGALCAGGWAVNYLPFFLMEKT
LFLYHYLPALTFQILLLPVVLQHISDHLCRSQLQRSIFSALVVAWYSSACHVSNTLRPLT
YGDKSLSPHELKALRWKDSWDILIRKH

Sequence length

747

Interactions

View interactions

	KEGG		Reactome
	Other types of O-glycan biosynthesis Mannose type O-glycan biosynthesis Metabolic pathways		Defective POMT2 causes MDDGA2, MDDGB2 and MDDGC2 Defective POMT1 causes MDDGA1, MDDGB1 and MDDGC1 O-linked glycosylation

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Congenital Muscular Dystrophy-Dystroglycanopathy With Brain And Eye Anomalies	Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1, Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1	rs587777819, rs777437871, rs587777820, rs398124245, rs1250351189, rs28941782, rs1554778005, rs1564341846, rs119462981, rs200056620, rs756973046, rs587777817, rs398124247, rs587777818, rs745738628 View all (6 more)	N/A
Limb-girdle muscular dystrophy	Autosomal recessive limb-girdle muscular dystrophy type 2K, Autosomal recessive limb-girdle muscular dystrophy	rs397514501, rs28941782, rs397515400, rs763586263, rs119462982, rs776988725, rs750195040	N/A
Walker-Warburg Congenital Muscular Dystrophy	walker-warburg congenital muscular dystrophy	rs1250351189	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
congenital muscular dystrophy	Congenital muscular dystrophy	N/A	N/A	ClinVar
Myopathy	myopathy caused by variation in POMT1	N/A	N/A	GenCC
Pyridoxine-Dependent Epilepsy	pyridoxine-dependent epilepsy	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (25)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acute Disease	Associate	29101272
Brain Diseases	Associate	22549409
Cardiomyopathies	Associate	22549409
Cardiomyopathy Dilated with Left Ventricular Noncompaction	Associate	22549409
Cataract Age Related Nuclear	Associate	12757935
Cognition Disorders	Associate	31311558
Cognitive Dysfunction	Associate	34565739
Complement Component C1s Deficiency	Associate	28157257
Congenital Microtia	Associate	30691450
Encephalocele	Associate	31311558
Ermine phenotype	Associate	26245304
Exercise Induced Allergies	Associate	34565739
Hydrocephalus	Associate	31311558
Intellectual Disability	Associate	22549409, 34565739
Malformations of Cortical Development Group II	Associate	12369018, 28953922
Microcephaly	Associate	31311558
Muscle Weakness	Associate	30060766
Muscular Diseases	Associate	34565739, 35606784
Muscular Dystrophies	Associate	22549409, 26245304, 28157257, 34565739
Muscular Dystrophies Limb Girdle	Associate	22549409, 31311558
Muscular dystrophy congenital with central nervous system involvement	Associate	34565739
Myopia	Associate	29346494
Nonsyndromic Deafness	Associate	29346494
Respiratory Insufficiency	Associate	22727687
Walker Warburg Syndrome	Associate	12369018, 12757935, 15894594, 16698797, 18752264, 19266496, 23217329, 29101272, 30060766, 31311558, 34565739

POMT1 (protein O-mannosyltransferase 1)