Human Gene POMT1 (ENST00000372228.9) from GENCODE V44
  Description: Homo sapiens protein O-mannosyltransferase 1 (POMT1), transcript variant 1, mRNA. (from RefSeq NM_007171)
RefSeq Summary (NM_007171): 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.[provided by RefSeq, Oct 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000372228.9
Gencode Gene: ENSG00000130714.19
Transcript (Including UTRs)
   Position: hg38 chr9:131,502,789-131,523,799 Size: 21,011 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg38 chr9:131,504,219-131,523,106 Size: 18,888 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:131,502,789-131,523,799)mRNA (may differ from genome)Protein (747 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: POMT1_HUMAN
DESCRIPTION: RecName: Full=Protein O-mannosyl-transferase 1; EC=2.4.1.109; AltName: Full=Dolichyl-phosphate-mannose--protein mannosyltransferase 1;
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.
CATALYTIC ACTIVITY: Dolichyl phosphate D-mannose + protein = dolichyl phosphate + O-D-mannosylprotein.
COFACTOR: Magnesium. Manganese and calcium ions suppress enzyme activity.
PATHWAY: Protein modification; protein glycosylation.
SUBUNIT: Interacts with POMT2 (Probable).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein.
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: Defects in POMT1 are the cause of muscular dystrophy- dystroglycanopathy congenital with mental retardation type B1 (MDDGB1) [MIM:613155]; also called muscular dystrophy congenital POMT1-related. MDDGB1 is an autosomal recessive disorder characterized by congenital muscular dystrophy associated with mental retardation and mild structural brain abnormalities.
DISEASE: Defects in POMT1 are the cause of muscular dystrophy- dystroglycanopathy congenital with brain and eye anomalies type A1 (MDDGA1) [MIM:236670]; also known as hydrocephalus-agyria-retinal dysplasia or HARD syndrome. MDDGA1 is an autosomal recessive disorder characterized by cobblestone lissencephaly, hydrocephalus, agyria, retinal displasia, with or without encephalocele. It is often associated with congenital muscular dystrophy and usually lethal within the first few months of life. Included diseases are the more severe Walker-Warburg syndrome and the slightly less severe muscle-eye-brain disease.
DISEASE: Defects in POMT1 are the cause of muscular dystrophy- dystroglycanopathy limb-girdle type C1 (MDDGC1) [MIM:609308]; also called autosomal recessive limb-girdle muscular dystrophy with mental retardation. MDDGC1 is a novel form of recessive limb girdle muscular dystrophy with mild mental retardation without any obvious structural brain abnormality, associated with an abnormal alpha-dystroglycan pattern in the muscle. MDDGC1 is a significantly milder allelic form of WWS.
SIMILARITY: Belongs to the glycosyltransferase 39 family.
SIMILARITY: Contains 3 MIR domains.
SEQUENCE CAUTION: Sequence=BAA91135.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA91190.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/POMT1";
WEB RESOURCE: Name=GGDB; Note=GlycoGene database; URL="http://riodb.ibase.aist.go.jp/rcmg/ggdb/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: POMT1
Diseases sorted by gene-association score: muscular dystrophy-dystroglycanopathy , type c, 1* (1568), muscular dystrophy-dystroglycanopathy , type a, 1* (1200), muscular dystrophy-dystroglycanopathy , type b, 1* (1200), congenital muscular dystrophy with cerebellar involvement* (350), congenital muscular dystrophy without intellectual disability* (350), congenital muscular dystrophy with intellectual disability* (247), walker-warburg syndrome* (238), pomt1-related muscle diseases* (200), muscle eye brain disease* (170), muscular dystrophy-dystroglycanopathy (18), muscular dystrophy (18), muscular dystrophy-dystroglycanopathy , type b, 5 (16), ablepharon-macrostomia syndrome (15), muscular dystrophy-dystroglycanopathy , type a, 4 (13), muscular dystrophy-dystroglycanopathy , type b, 6 (13), muscular dystrophy-dystroglycanopathy , type c, 2 (8), autosomal recessive limb-girdle muscular dystrophy (8), muscular dystrophy, limb-girdle, type 2l (7), cobblestone lissencephaly (7), muscular dystrophy, congenital (6), microcephaly (2), congenital nervous system abnormality (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.91 RPKM in Testis
Total median expression: 330.31 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -146.30315-0.464 Picture PostScript Text
3' UTR -258.80693-0.373 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR027005 - GlyclTrfase_39
IPR003342 - Glyco_trans_39
IPR016093 - MIR_motif

Pfam Domains:
PF02815 - MIR domain
PF02366 - Dolichyl-phosphate-mannose-protein mannosyltransferase

ModBase Predicted Comparative 3D Structure on Q9Y6A1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000030 mannosyltransferase activity
GO:0004169 dolichyl-phosphate-mannose-protein mannosyltransferase activity
GO:0016740 transferase activity
GO:0016757 transferase activity, transferring glycosyl groups
GO:0046872 metal ion binding

Biological Process:
GO:0005975 carbohydrate metabolic process
GO:0006486 protein glycosylation
GO:0006493 protein O-linked glycosylation
GO:0007275 multicellular organism development
GO:0030198 extracellular matrix organization
GO:0035269 protein O-linked mannosylation
GO:0071712 ER-associated misfolded protein catabolic process
GO:0097502 mannosylation
GO:1904100 positive regulation of protein O-linked glycosylation

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0016529 sarcoplasmic reticulum


-  Descriptions from all associated GenBank mRNAs
  KJ898249 - Synthetic construct Homo sapiens clone ccsbBroadEn_07643 POMT1 gene, encodes complete protein.
LF346798 - JP 2014500723-A/154301: Polycomb-Associated Non-Coding RNAs.
MA582375 - JP 2018138019-A/154301: Polycomb-Associated Non-Coding RNAs.
AK295561 - Homo sapiens cDNA FLJ59534 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
HM005680 - Homo sapiens clone HTL-T-57p testis tissue sperm-binding protein Li 57p mRNA, complete cds.
LF205643 - JP 2014500723-A/13146: Polycomb-Associated Non-Coding RNAs.
MA441220 - JP 2018138019-A/13146: Polycomb-Associated Non-Coding RNAs.
AK074888 - Homo sapiens cDNA FLJ90407 fis, clone NT2RP2006269, highly similar to Protein O-mannosyl-transferase 1 (EC2.4.1.109).
AK301486 - Homo sapiens cDNA FLJ57215 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC2.4.1.109).
AF095136 - Homo sapiens protein O-mannosyl-transferase 1 (POMT1) mRNA, complete cds.
AK307876 - Homo sapiens cDNA, FLJ97824.
AK303254 - Homo sapiens cDNA FLJ59105 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
AK074874 - Homo sapiens cDNA FLJ90393 fis, clone NT2RP2005597, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
AK299646 - Homo sapiens cDNA FLJ58261 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
AK295458 - Homo sapiens cDNA FLJ59530 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
AK300393 - Homo sapiens cDNA FLJ59427 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
BC065268 - Homo sapiens protein-O-mannosyltransferase 1, mRNA (cDNA clone MGC:74644 IMAGE:6155142), complete cds.
AK315218 - Homo sapiens cDNA, FLJ96212.
AK293529 - Homo sapiens cDNA FLJ57950 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
BC022877 - Homo sapiens protein-O-mannosyltransferase 1, mRNA (cDNA clone MGC:26278 IMAGE:4826806), complete cds.
JD484988 - Sequence 466012 from Patent EP1572962.
KX098451 - Homo sapiens truncated O-mannosyl-transferase 1 variant SV3DEL (POMT1) mRNA, complete cds, alternatively spliced.
LC030233 - Homo sapiens POMT1 mRNA, complete cds, contains 9-bp deletion.
AB209430 - Homo sapiens premature mRNA for protein O-mannosyl-transferase 1 variant.
AK000391 - Homo sapiens cDNA FLJ20384 fis, clone KAIA2967.
LF346801 - JP 2014500723-A/154304: Polycomb-Associated Non-Coding RNAs.
MA582378 - JP 2018138019-A/154304: Polycomb-Associated Non-Coding RNAs.
LF346802 - JP 2014500723-A/154305: Polycomb-Associated Non-Coding RNAs.
MA582379 - JP 2018138019-A/154305: Polycomb-Associated Non-Coding RNAs.
AK300511 - Homo sapiens cDNA FLJ58425 complete cds, highly similar to Protein O-mannosyl-transferase 1 (EC 2.4.1.109).
LF346805 - JP 2014500723-A/154308: Polycomb-Associated Non-Coding RNAs.
MA582382 - JP 2018138019-A/154308: Polycomb-Associated Non-Coding RNAs.
AK094558 - Homo sapiens cDNA FLJ37239 fis, clone BRAMY2003897, highly similar to Protein-O-mannosyltransferase 1.
LF346808 - JP 2014500723-A/154311: Polycomb-Associated Non-Coding RNAs.
MA582385 - JP 2018138019-A/154311: Polycomb-Associated Non-Coding RNAs.
LF346809 - JP 2014500723-A/154312: Polycomb-Associated Non-Coding RNAs.
MA582386 - JP 2018138019-A/154312: Polycomb-Associated Non-Coding RNAs.
LF346810 - JP 2014500723-A/154313: Polycomb-Associated Non-Coding RNAs.
MA582387 - JP 2018138019-A/154313: Polycomb-Associated Non-Coding RNAs.
AK000475 - Homo sapiens cDNA FLJ20468 fis, clone KAT06772.
LF346811 - JP 2014500723-A/154314: Polycomb-Associated Non-Coding RNAs.
MA582388 - JP 2018138019-A/154314: Polycomb-Associated Non-Coding RNAs.
LF346812 - JP 2014500723-A/154315: Polycomb-Associated Non-Coding RNAs.
MA582389 - JP 2018138019-A/154315: Polycomb-Associated Non-Coding RNAs.
LF346813 - JP 2014500723-A/154316: Polycomb-Associated Non-Coding RNAs.
MA582390 - JP 2018138019-A/154316: Polycomb-Associated Non-Coding RNAs.
LF346815 - JP 2014500723-A/154318: Polycomb-Associated Non-Coding RNAs.
MA582392 - JP 2018138019-A/154318: Polycomb-Associated Non-Coding RNAs.
JD396811 - Sequence 377835 from Patent EP1572962.
JD048643 - Sequence 29667 from Patent EP1572962.
JD100640 - Sequence 81664 from Patent EP1572962.
JD466475 - Sequence 447499 from Patent EP1572962.
JD287329 - Sequence 268353 from Patent EP1572962.
JD433954 - Sequence 414978 from Patent EP1572962.
JD310269 - Sequence 291293 from Patent EP1572962.
JD039655 - Sequence 20679 from Patent EP1572962.
JD134080 - Sequence 115104 from Patent EP1572962.
JD421008 - Sequence 402032 from Patent EP1572962.
JD211615 - Sequence 192639 from Patent EP1572962.
JD510806 - Sequence 491830 from Patent EP1572962.
JD274813 - Sequence 255837 from Patent EP1572962.
JD036921 - Sequence 17945 from Patent EP1572962.
LF346817 - JP 2014500723-A/154320: Polycomb-Associated Non-Coding RNAs.
MA582394 - JP 2018138019-A/154320: Polycomb-Associated Non-Coding RNAs.
JD555590 - Sequence 536614 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00514 - O-Mannosyl glycan biosynthesis

Reactome (by CSHL, EBI, and GO)

Protein Q9Y6A1 (Reactome details) participates in the following event(s):

R-HSA-5615637 POMT1:POMT2 transfers Man from Dol-P-Man to DAG1(30-653)
R-HSA-5173105 O-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B3KQG0, B4DIF0, ENST00000372228.1, ENST00000372228.2, ENST00000372228.3, ENST00000372228.4, ENST00000372228.5, ENST00000372228.6, ENST00000372228.7, ENST00000372228.8, NM_007171, POMT1_HUMAN, Q5JT01, Q5JT06, Q5JT08, Q8NC91, Q8TCA9, Q9NX32, Q9NX82, Q9UNT2, Q9Y6A1, uc004cav.1, uc004cav.2, uc004cav.3, uc004cav.4, uc004cav.5, uc004cav.6
UCSC ID: ENST00000372228.9
RefSeq Accession: NM_007171
Protein: Q9Y6A1 (aka POMT1_HUMAN or POT1_HUMAN)
CCDS: CCDS6943.1, CCDS43894.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.