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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	10585
Gene name	Protein O-mannosyltransferase 1
Gene symbol	POMT1
Synonyms (NCBI Gene)	LGMD2KLGMDR11MDDGA1MDDGB1MDDGC1RT
Chromosome	9
Chromosome location	9q34.13
Summary	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

Show/Hide all (51)

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

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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

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

3174

Show/Hide Causal Diseases (17)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal brainstem morphology	Pathogenic	rs398124245	RCV001391256
Abnormality of the musculature	Pathogenic	rs119462981	RCV001813941
Abnormality of the nervous system	Likely pathogenic; Pathogenic	rs119462982	RCV001813942
Autosomal recessive limb-girdle muscular dystrophy	Pathogenic; Likely pathogenic	rs200056620, rs398124244, rs2131751359, rs1554772469, rs1950265792, rs28941782, rs119462982, rs119462983, rs119462986, rs398124245, rs794727190, rs763586263, rs1032439203	RCV004689449 RCV005431467 RCV001553600 RCV004529018 RCV001844648 RCV005055501 RCV003234890 RCV005887254 RCV006262331 RCV003398430 RCV003230434 RCV002469286 RCV004702574
Autosomal recessive limb-girdle muscular dystrophy type 2K	Pathogenic; Likely pathogenic	rs200056620, rs398124244, rs398124247, rs760071332, rs746523421, rs2131588122, rs2131749139, rs2131751359, rs747129906, rs1554772469, rs1950265792, rs759848847, rs2131672013, rs2131554631, rs766648827 View all (98 more)	RCV000686940 RCV001376971 RCV002513831 RCV001378932 RCV001377161 RCV001391024 RCV001388909 RCV003771694 RCV002544255 RCV003772194 RCV002034732 RCV001893866 RCV001894437 RCV001937387 RCV001964400 RCV002037840 RCV001993223 RCV002036317 RCV001949458 RCV001872394 RCV002019789 RCV003094035 RCV003764901 RCV003764521 RCV000003399 RCV002512705 RCV001851614 RCV003764522 RCV000694423 RCV001383583 RCV005041977 RCV000546035 RCV002595666 RCV002516666 RCV000704810 RCV003104711 RCV002645716 RCV002791664 RCV002815003 RCV002815007 RCV002846242 RCV002857255 RCV002891143 RCV002517157 RCV002957729 RCV003039275 RCV003779070 RCV005047604 RCV005864671 RCV005051311 RCV005047605 RCV005051312 RCV003779074 RCV005051313 RCV005051314 RCV003785381 RCV003783725 RCV003798174 RCV003795840 RCV003780596 RCV003781106 RCV003781107 RCV003789850 RCV003793280 RCV003780014 RCV003789429 RCV003806219 RCV003806741 RCV003806891 RCV003803374 RCV003800866 RCV003808697 RCV003804863 RCV003802423 RCV003817774 RCV003807309 RCV003807330 RCV003807421 RCV003812328 RCV003802574 RCV003810229 RCV003810451 RCV002525809 RCV000850367 RCV005049585 RCV003766974 RCV000548536 RCV000558807 RCV000032629 RCV000032630 RCV000763189 RCV002529346 RCV000648156 RCV004554817 RCV000703521 RCV000704477 RCV000799994 RCV001040545 RCV000791485 RCV000815478 RCV000811436 RCV001869305 RCV000988265 RCV001862754 RCV001071806 RCV001052576 RCV003769027 RCV001201840 RCV001205242 RCV001217576 RCV001228965 RCV001235411 RCV001225759 RCV003770344 RCV002537636
Dysgenesis of the cerebellar vermis	Pathogenic	rs1564325733, rs1945766589	RCV001257390 RCV001257391
Limb-girdle muscular dystrophy due to POMK deficiency	Pathogenic	rs200056620	RCV002288580
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1	Pathogenic; Likely pathogenic	rs200056620, rs398124244, rs398124247, rs746523421, rs745509085, rs2131751359, rs2131708682, rs1554772469, rs1950265792, rs759848847, rs1472946513, rs1397478363, rs1222795311, rs1289335417, rs961071228 View all (82 more)	RCV002498428 RCV003474682 RCV003474683 RCV003462945 RCV003474001 RCV003474006 RCV001844391 RCV005040388 RCV003475106 RCV003475152 RCV005050480 RCV003475244 RCV004571441 RCV003464372 RCV002250254 RCV002267187 RCV002267189 RCV000003394 RCV000003395 RCV000003396 RCV000003397 RCV003472966 RCV003460408 RCV005041976 RCV003460409 RCV003472967 RCV000003408 RCV000003410 RCV000003411 RCV003475391 RCV004572793 RCV004567379 RCV003474928 RCV003474929 RCV005045039 RCV000192686 RCV003475887 RCV003475575 RCV003463357 RCV003463358 RCV003463359 RCV003463360 RCV003463362 RCV003463363 RCV003471733 RCV003463364 RCV003471734 RCV003471735 RCV003463365 RCV003463366 RCV003463367 RCV003472483 RCV003472484 RCV003472486 RCV003472487 RCV003472489 RCV003472490 RCV003472491 RCV003472493 RCV003472494 RCV003472495 RCV003472496 RCV003472497 RCV003472499 RCV003472500 RCV004573332 RCV005040528 RCV003989918 RCV004574603 RCV004574604 RCV004574605 RCV004574606 RCV004574607 RCV004574608 RCV004574609 RCV004574610 RCV004594822 RCV003464000 RCV003476193 RCV005049585 RCV003476298 RCV003459248 RCV000763189 RCV003471973 RCV003459477 RCV003459544 RCV004554817 RCV002485867 RCV003465669 RCV003461048 RCV000790413 RCV000853233 RCV003461312 RCV003462625 RCV003473715 RCV004570568 RCV003473785 RCV001262622
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1	Pathogenic; Likely pathogenic	rs200056620, rs398124244, rs398124247, rs760071332, rs746523421, rs2131588122, rs2131749139, rs1564395473, rs2131751359, rs747129906, rs1554772469, rs1950265792, rs759848847, rs2131672013, rs2131554631 View all (97 more)	RCV000578428 RCV001376971 RCV002513831 RCV001378932 RCV001377161 RCV001391024 RCV001388909 RCV001420148 RCV003771694 RCV002544255 RCV003772194 RCV002034732 RCV001893866 RCV001894437 RCV001937387 RCV001964400 RCV002037840 RCV001993223 RCV002036317 RCV001949458 RCV001872394 RCV002019789 RCV003094035 RCV003764901 RCV003764521 RCV001385876 RCV002512705 RCV001851614 RCV002286391 RCV000694423 RCV001383583 RCV000587199 RCV000546035 RCV002595666 RCV002516666 RCV000704810 RCV003104711 RCV002645716 RCV002791664 RCV002815003 RCV002815007 RCV002846242 RCV002857255 RCV002891143 RCV002517157 RCV002957729 RCV003039275 RCV003779070 RCV005047604 RCV005051311 RCV005047605 RCV005051312 RCV003779074 RCV005051313 RCV005051314 RCV003785381 RCV003783725 RCV003798174 RCV003795840 RCV003780596 RCV003781106 RCV003781107 RCV003789850 RCV003793280 RCV003780014 RCV003789429 RCV003806219 RCV003806741 RCV003806891 RCV003803374 RCV003800866 RCV003808697 RCV003804863 RCV003802423 RCV003817774 RCV003807309 RCV003807330 RCV003807421 RCV003812328 RCV003802574 RCV003810229 RCV003810451 RCV002525809 RCV001205238 RCV005049585 RCV003766974 RCV000548536 RCV000558807 RCV000578259 RCV000763189 RCV002529346 RCV000648156 RCV004554817 RCV000761585 RCV000703521 RCV000704477 RCV000799994 RCV001040545 RCV000791485 RCV000815478 RCV000811436 RCV001869305 RCV001862754 RCV001071806 RCV001052576 RCV003769027 RCV001201840 RCV001205242 RCV001217576 RCV001228965 RCV001235411 RCV001225759 RCV003770344 RCV002537636
Muscular dystrophy-dystroglycanopathy, type C	Pathogenic	rs398124245	RCV003225921
Myopathy caused by variation in POMT1	Pathogenic; Likely pathogenic	rs398124247, rs1564365317	RCV003314560 RCV006257315
Ovarian serous cystadenocarcinoma	Likely pathogenic; Pathogenic	rs746523421	RCV005912587
POMT1-related disorder	Likely pathogenic; Pathogenic	rs398124244, rs398124245, rs746161025	RCV004529856 RCV000778874 RCV004534404
Thymoma	Likely pathogenic; Pathogenic	rs961071228	RCV005930062
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs746523421	RCV005912588
Ventriculomegaly	Pathogenic	rs398124245	RCV001391256
Walker-Warburg congenital muscular dystrophy	Pathogenic; Likely pathogenic	rs200056620, rs398124244, rs398124247, rs760071332, rs746523421, rs2131588122, rs2131749139, rs745509085, rs2131751359, rs747129906, rs1554772469, rs1950265792, rs759848847, rs2131672013, rs2131554631 View all (90 more)	RCV000686940 RCV001376971 RCV002513831 RCV001378932 RCV001377161 RCV001391024 RCV001388909 RCV001449743 RCV003771694 RCV002544255 RCV003772194 RCV002034732 RCV001893866 RCV001894437 RCV001937387 RCV001964400 RCV002037840 RCV001993223 RCV002036317 RCV001949458 RCV001872394 RCV002019789 RCV003094035 RCV003764901 RCV003764521 RCV001385876 RCV002512705 RCV001851614 RCV003764522 RCV000694423 RCV001383583 RCV000546035 RCV002595666 RCV002516666 RCV000704810 RCV003104711 RCV002645716 RCV002791664 RCV002815003 RCV002815007 RCV002846242 RCV002857255 RCV002891143 RCV002517157 RCV002957729 RCV003039275 RCV003779070 RCV003779071 RCV003779072 RCV003779073 RCV003779074 RCV003785381 RCV003783725 RCV003798174 RCV003795840 RCV003780596 RCV003781106 RCV003781107 RCV003789850 RCV003793280 RCV003780014 RCV003789429 RCV003806219 RCV003806741 RCV003806891 RCV003803374 RCV003800866 RCV003808697 RCV003804863 RCV003802423 RCV003817774 RCV003807309 RCV003807330 RCV003807421 RCV003812328 RCV003802574 RCV003810229 RCV003810451 RCV004018306 RCV002525809 RCV001205238 RCV003766974 RCV000548536 RCV000558807 RCV003767405 RCV000608987 RCV000648156 RCV000703521 RCV000704477 RCV000799994 RCV001040545 RCV000791485 RCV000815478 RCV000811436 RCV001869305 RCV001862754 RCV001071806 RCV001052576 RCV003769027 RCV001201840 RCV001205242 RCV001217576 RCV001228965 RCV001235411 RCV001225759 RCV003770344 RCV002537636

Show/Hide Unknown Diseases (29)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs756975009	-
Acute myeloid leukemia	Benign; Likely benign	rs140258585, rs148180760	RCV005889204 RCV005889217
Cerebellar ataxia	Uncertain significance	rs202140413	RCV000415416
Cervical cancer	Benign; Likely benign	rs140258585, rs148180760	RCV005889207 RCV005889220
Colon adenocarcinoma	Uncertain significance	rs139774354	RCV005895858
Congenital muscular dystrophy	Benign; Likely benign; Uncertain significance	rs148086540, rs727502853	RCV000150009 RCV000150014
FAM157B-related disorder	Benign; Likely benign	rs146512619	RCV003939984
Familial cancer of breast	Benign; Likely benign	rs140258585, rs148180760	RCV005889203 RCV005889216
Gait disturbance	Uncertain significance	rs202140413	RCV000415416
Gastric cancer	Benign; Likely benign; -; Uncertain significance	rs140258585, rs148180760, rs2131683729, rs756531223	RCV005889210 RCV005889223 RCV005930207 RCV005912470
Hearing impairment	Uncertain significance	rs202140413	RCV000415416
Intellectual disability	Conflicting classifications of pathogenicity	rs117985576	RCV001252355
Limb-girdle muscular dystrophy, recessive	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs148086540, rs761863400, rs748211086, rs886063540	RCV000265747 RCV000327854 RCV000384984 RCV000260773 RCV000369129
Lung cancer	Benign; Likely benign	rs140258585, rs148180760	RCV005889214 RCV005889227
Lymphoma	Benign; Likely benign	rs140258585, rs148180760	RCV005889211 RCV005889224
Malignant tumor of esophagus	Benign; Likely benign	rs140258585, rs148180760	RCV005889205 RCV005889218
Melanoma	Uncertain significance	rs1417849652, rs139774354	RCV005928310 RCV005895859
Neurodevelopmental abnormality	Uncertain significance	rs369644530	RCV001264687
Nonpapillary renal cell carcinoma	Benign; Likely benign	rs140258585, rs148180760, rs148086540	RCV005889206 RCV005889219 RCV005871320
Ovarian cancer	Benign; Likely benign	rs140258585, rs148180760	RCV005889208 RCV005889221
POMT1-related congenital myopathy	Conflicting classifications of pathogenicity	rs377372480, rs757903559	RCV004586544 RCV004586824
Poor speech	Uncertain significance	rs202140413	RCV000415416
Pyridoxine-dependent epilepsy	Uncertain significance	rs201073763	RCV000678830
Sarcoma	Benign; Likely benign	rs140258585, rs148180760	RCV005889209 RCV005889222
Seizure	Uncertain significance	rs141229412	RCV000626903
Sensory neuropathy	Uncertain significance	rs202140413	RCV000415416
Severe global developmental delay	Uncertain significance	rs141229412	RCV000626903
Squamous cell carcinoma of the head and neck	Uncertain significance	rs772980661	RCV005912275
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs140258585, rs148180760, rs111470256	RCV005889215 RCV005889228 RCV005908831

Show/Hide Text Mining Associations (25)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)