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    MDGA1 MAM domain containing glycosylphosphatidylinositol anchor 1 [ Homo sapiens (human) ]

    Gene ID: 266727, updated on 28-Oct-2024

    Summary

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    Official Symbol
    MDGA1provided by HGNC
    Official Full Name
    MAM domain containing glycosylphosphatidylinositol anchor 1provided by HGNC
    Primary source
    HGNC:HGNC:19267
    See related
    Ensembl:ENSG00000112139 MIM:609626; AllianceGenome:HGNC:19267
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    GPIM; MAMDC3
    Summary
    This gene encodes a glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein that is expressed predominantly in the developing nervous system. In addition to possessing several cell adhesion molecule-like domains, the mature protein has six Ig-like domains, a single fibronectin type III domain, a MAM domain and a C-terminal GPI-anchoring site. Studies in other mammals suggest this protein plays a role in cell adhesion, migration, and axon guidance and, in the developing brain, neuronal migration. In humans, this gene is associated with bipolar disorder and schizophrenia. [provided by RefSeq, Oct 2016]
    Expression
    Broad expression in brain (RPKM 2.6), ovary (RPKM 2.3) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See MDGA1 in Genome Data Viewer
    Location:
    6p21.2
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (37630679..37697883, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (37455697..37522898, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (37598455..37665659, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17142 Neighboring gene uncharacterized LOC124901313 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37551989-37552662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37552663-37553335 Neighboring gene microRNA 4462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17144 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37663553-37664282 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17149 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37664283-37665012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17151 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17152 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37695835-37696335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24478 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37717757-37718578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37730195-37730696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37744227-37744777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:37744845-37745776 Neighboring gene Sharpr-MPRA regulatory regions 13021 and 15353 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24480 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:37787069-37787871 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17156 Neighboring gene ZFAND3 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 285, pseudogene Neighboring gene zinc finger AN1-type containing 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. The MDGA1 gene confers risk to schizophrenia and bipolar disorder. Li J, et al. Schizophr Res, 2011 Feb. PMID 21146959
    2. Genomic organization of a novel glycosylphosphatidylinositol MAM gene expressed in human tissues and tumors. De Juan C, et al. Oncogene, 2002 May 2. PMID 12082541
    3. Characterization of MDGA1, a novel human glycosylphosphatidylinositol-anchored protein localized in lipid rafts. Díaz-López A, et al. Exp Cell Res, 2005 Jul 1. PMID 15922729
    4. Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges. Gangwar SP, et al. Neuron, 2017 Jun 21. PMID 28641112, Free PMC Article
    5. MDGAs interact selectively with neuroligin-2 but not other neuroligins to regulate inhibitory synapse development. Lee K, et al. Proc Natl Acad Sci U S A, 2013 Jan 2. PMID 23248271, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. MDGAs regulate the formation of neuroligin-neurexin trans-synaptic bridges by sterically blocking access of neurexins to neuroligins.
      Title: Molecular Mechanism of MDGA1: Regulation of Neuroligin 2:Neurexin Trans-synaptic Bridges.
    2. The MDGA1 gene may confer risk to schizophrenia and bipolar disorder in Chinese Han population.
      Title: The MDGA1 gene confers risk to schizophrenia and bipolar disorder.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. MDGA1 is a new schizophrenia susceptibility gene, and altered neuronal migration is involved in SZ pathology.
      Title: Association analysis of schizophrenia on 18 genes involved in neuronal migration: MDGA1 as a new susceptibility gene.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association analysis of schizophrenia on 18 genes involved in neuronal migration: MDGA1 as a new susceptibility gene.
    6. MDGA1, a novel glycosylphosphatidylinositol-anchored protein, is localized in lipid rafts.
      Title: Characterization of MDGA1, a novel human glycosylphosphatidylinositol-anchored protein localized in lipid rafts.
    7. A novel human gene mapped to chromosome 6p21, encodes a putative glycosylphosphatidylinositol (GPI) anchored protein containing a MAM (meprin, A5 antigen, protein tyrosine phosphatase mu) domain. (GPIM)
      Title: Genomic organization of a novel glycosylphosphatidylinositol MAM gene expressed in human tissues and tumors.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ45018, DKFZp686K0262, DKFZp686L0262

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in brain development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    involved_in cerebral cortex radially oriented cell migration IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inhibitory synapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron migration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of presynapse assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of presynapse assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of synaptic membrane adhesion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synaptic membrane adhesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spinal cord association neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in GABA-ergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in GABA-ergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular space HDA PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    MAM domain-containing glycosylphosphatidylinositol anchor protein 1
    Names
    GPI and MAM protein
    MAM domain-containing protein 3
    glycosylphosphatidylinositol-MAM

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_051764.1 RefSeqGene

      Range
      5108..72312
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_153487.4 → NP_705691.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 preproprotein

      See identical proteins and their annotated locations for NP_705691.1

      Status: REVIEWED

      Source sequence(s)
      AF478693, AL049553
      Consensus CDS
      CCDS47417.1
      UniProtKB/Swiss-Prot
      A6NHG0, Q8NBE3, Q8NFP4
      UniProtKB/TrEMBL
      A0A3B3IU48
      Related
      ENSP00000402584.2, ENST00000434837.8
      Conserved Domains (6) summary
      smart00409
      Location:248 → 326
      IG; Immunoglobulin
      smart00410
      Location:152 → 217
      IG_like; Immunoglobulin like
      pfam00629
      Location:753 → 917
      MAM; MAM domain, meprin/A5/mu
      pfam13927
      Location:43 → 112
      Ig_3; Immunoglobulin domain
      cd00096
      Location:56 → 60
      Ig; Ig strand B [structural motif]
      cl11960
      Location:334 → 418
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      37630679..37697883 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017010734.2 → XP_016866223.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A3B3IU48
      Conserved Domains (6) summary
      smart00409
      Location:248 → 326
      IG; Immunoglobulin
      smart00410
      Location:152 → 217
      IG_like; Immunoglobulin like
      pfam00629
      Location:753 → 917
      MAM; MAM domain, meprin/A5/mu
      pfam13927
      Location:43 → 112
      Ig_3; Immunoglobulin domain
      cd00096
      Location:56 → 60
      Ig; Ig strand B [structural motif]
      cl11960
      Location:334 → 418
      Ig; Immunoglobulin domain

    2. XM_006715056.4 → XP_006715119.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006715119.1

      UniProtKB/TrEMBL
      A0A3B3IU48
      Related
      ENSP00000422042.1, ENST00000505425.5
      Conserved Domains (6) summary
      cd06263
      Location:753 → 916
      MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...
      cd00096
      Location:153 → 217
      Ig; Immunoglobulin domain
      smart00408
      Location:254 → 315
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:248 → 326
      IG_like; Immunoglobulin like
      pfam00629
      Location:753 → 917
      MAM; MAM domain, meprin/A5/mu
      cl11960
      Location:541 → 622
      Ig; Immunoglobulin domain

    3. XM_047418637.1 → XP_047274593.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X3

    4. XM_047418638.1 → XP_047274594.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A7P0TB62
      Related
      ENSP00000506519.1, ENST00000681472.1

    RNA

    1. XR_926141.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      37455697..37522898 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054355158.1 → XP_054211133.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X2

    2. XM_054355157.1 → XP_054211132.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X1

    3. XM_054355159.1 → XP_054211134.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X3

    4. XM_054355160.1 → XP_054211135.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A7P0TB62

    RNA

    1. XR_008487298.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NFP4.1 GenPept UniProtKB/Swiss-Prot:Q8NFP4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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