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    MDGA2 MAM domain containing glycosylphosphatidylinositol anchor 2 [ Homo sapiens (human) ]

    Gene ID: 161357, updated on 28-Oct-2024

    Summary

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    Official Symbol
    MDGA2provided by HGNC
    Official Full Name
    MAM domain containing glycosylphosphatidylinositol anchor 2provided by HGNC
    Primary source
    HGNC:HGNC:19835
    See related
    Ensembl:ENSG00000139915 MIM:611128; AllianceGenome:HGNC:19835
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MAMDC1; c14_5286
    Summary
    Predicted to be involved in regulation of synapse organization and spinal cord motor neuron differentiation. Predicted to act upstream of or within several processes, including motor behavior; negative regulation of neuron apoptotic process; and neuron migration. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in brain (RPKM 1.3) and testis (RPKM 0.6) See more
    Orthologs
    mouse all
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    Genomic context

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    See MDGA2 in Genome Data Viewer
    Location:
    14q21.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (46839623..47675605, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (41038514..41874449, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (47308826..48144808, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903309 Neighboring gene uncharacterized LOC105370480 Neighboring gene uncharacterized LOC105370481 Neighboring gene MPRA-validated peak2148 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr14:47215033-47215240 Neighboring gene ribosomal protein L10 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8308 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr14:47287501-47288032 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:47354646-47355845 Neighboring gene MPRA-validated peak2151 silencer Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:47572669-47573230 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:47573231-47573790 Neighboring gene replication protein A2 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:47577386-47578367 Neighboring gene MPRA-validated peak2152 silencer Neighboring gene ribosomal protein L13a pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5695 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:47769492-47770691 Neighboring gene NANOG hESC enhancer GRCh37_chr14:47858750-47859440 Neighboring gene ribosomal protein S15a pseudogene 3 Neighboring gene NANOG hESC enhancer GRCh37_chr14:48005441-48006008 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:48034589-48035090 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:48035091-48035590 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:48088147-48089346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:48145545-48146044 Neighboring gene kinesin family member 20B pseudogene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr14:48263841-48264342 Neighboring gene long intergenic non-protein coding RNA 648 Neighboring gene microRNA 548y

    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. Follow-up association study of novel neuroticism gene MAMDC1. Hettema JM, et al. Psychiatr Genet, 2009 Aug. PMID 19440164, Free PMC Article
    2. Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE). Hellquist A, et al. PLoS One, 2009 Dec 7. PMID 19997561, Free PMC Article
    3. Evidence for associations between MDGA2 polymorphisms and harm avoidance: replication and extension of a genome-wide association finding. Heck A, et al. Psychiatr Genet, 2011 Oct. PMID 21399569
    4. Rostral growth of commissural axons requires the cell adhesion molecule MDGA2. Joset P, et al. Neural Dev, 2011 May 4. PMID 21542908, Free PMC Article
    5. Single-nucleotide polymorphisms of MAMDC1 are associated with rash and photosensitivity, but not disease risk, of systemic lupus erythematosus in Chinese mainland population. Wu Q, et al. Clin Rheumatol, 2011 Oct. PMID 21660437

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A novel tumour suppressor gene, MDGA2, which is frequently inactivated by promoter methylation in Gastric cancer was identified. Promoter hypermethylation of MDGA2 represents a prognostic biomarker in patients with early stage Gastric cancer.
      Title: MDGA2 is a novel tumour suppressor cooperating with DMAP1 in gastric cancer and is associated with disease outcome.
    2. This finding provides further support for a link between variants in the MDGA2 gene and specific neuroticism-related phenotypes.
      Title: Evidence for associations between MDGA2 polymorphisms and harm avoidance: replication and extension of a genome-wide association finding.
    3. Polymorphisms of rs961616 in MAMDC1 gene were associated with rash and photosensitivity, but not disease risk, of systemic lupus erythematosus in Chinese population.
      Title: Single-nucleotide polymorphisms of MAMDC1 are associated with rash and photosensitivity, but not disease risk, of systemic lupus erythematosus in Chinese mainland population.
    4. This study demonistrated suggested taht Rostral growth of commissural axons requires the cell adhesion molecule MDGA2
      Title: Rostral growth of commissural axons requires the cell adhesion molecule MDGA2.
    5. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    6. 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.
    7. A novel uncharacterized gene, MAMDC1 (MAM domain containing glycosylphosphatidylinositol anchor 2, also known as MDGA2, MIM 611128), represents a putative susceptibility gene for systemic lupus erythematosus.
      Title: Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE).
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Identification of MAMDC1 as a candidate susceptibility gene for systemic lupus erythematosus (SLE).
    9. No association of rs7151262 with neuroticism was found
      Title: Follow-up association study of novel neuroticism gene MAMDC1.
    10. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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
    Genetic variants associated with idiopathic pulmonary fibrosis susceptibility and mortality: a genome-wide association study.
    EBI GWAS Catalog
    Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis.
    EBI GWAS Catalog
    Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study.
    EBI GWAS Catalog
    Genome-wide association study of SSRI/SNRI-induced sexual dysfunction in a Japanese cohort with major depression.
    EBI GWAS Catalog
    Genomewide association analysis followed by a replication study implicates a novel candidate gene for neuroticism.
    EBI GWAS Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in spinal cord motor neuron differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    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 2
    Names
    MAM domain containing 1

    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.

    mRNA and Protein(s)

    1. NM_001113498.3 → NP_001106970.4  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL157792, AL162551, AL358832, AL359951, AL591771
      Consensus CDS
      CCDS45098.4
      UniProtKB/Swiss-Prot
      F6W3S7, J3KPX6, Q7Z553
      Related
      ENSP00000382178.4, ENST00000399232.8
      Conserved Domains (6) summary
      smart00408
      Location:325 → 386
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:117 → 197
      IG; Immunoglobulin
      pfam00629
      Location:817 → 989
      MAM; MAM domain, meprin/A5/mu
      pfam13927
      Location:510 → 587
      Ig_3; Immunoglobulin domain
      cd00096
      Location:511 → 514
      Ig; Ig strand A [structural motif]
      cl11960
      Location:418 → 493
      Ig; Immunoglobulin domain

    2. NM_182830.4 → NP_878250.2  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform 2

      See identical proteins and their annotated locations for NP_878250.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and has multiple 5' coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL591771, AY369208, BC028193, DB095976
      Consensus CDS
      CCDS41948.1
      Conserved Domains (6) summary
      cd06263
      Location:519 → 690
      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:126 → 198
      Ig; Immunoglobulin domain
      smart00408
      Location:27 → 88
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:222 → 307
      IG_like; Immunoglobulin like
      pfam00629
      Location:519 → 692
      MAM; MAM domain, meprin/A5/mu
      pfam13895
      Location:314 → 389
      Ig_2; Immunoglobulin domain

    RNA

    1. NR_103766.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL359951, BC028193, DB095976
      Related
      ENST00000482848.7

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      46839623..47675605 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011536519.3 → XP_011534821.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X1

      UniProtKB/Swiss-Prot
      F6W3S7, J3KPX6, Q7Z553
      Conserved Domains (6) summary
      cd06263
      Location:772 → 943
      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:379 → 451
      Ig; Immunoglobulin domain
      smart00408
      Location:280 → 341
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:72 → 152
      IG_like; Immunoglobulin like
      pfam00629
      Location:772 → 945
      MAM; MAM domain, meprin/A5/mu
      pfam13895
      Location:567 → 642
      Ig_2; Immunoglobulin domain

    2. XM_047431048.1 → XP_047287004.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

      Related
      ENSP00000349925.3, ENST00000357362.7

    3. XM_047431049.1 → XP_047287005.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

    4. XM_047431050.1 → XP_047287006.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

    5. XM_017021060.2 → XP_016876549.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X4

      UniProtKB/Swiss-Prot
      Q7Z553
      Conserved Domains (5) summary
      cd06263
      Location:363 → 534
      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 ...
      smart00408
      Location:72 → 137
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:66 → 151
      IG_like; Immunoglobulin like
      pfam00629
      Location:363 → 536
      MAM; MAM domain, meprin/A5/mu
      pfam13895
      Location:158 → 233
      Ig_2; Immunoglobulin domain

    6. XM_011536525.3 → XP_011534827.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X7

      Conserved Domains (5) summary
      cd06263
      Location:308 → 479
      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 ...
      smart00408
      Location:17 → 82
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:11 → 96
      IG_like; Immunoglobulin like
      pfam00629
      Location:308 → 481
      MAM; MAM domain, meprin/A5/mu
      pfam13895
      Location:103 → 178
      Ig_2; Immunoglobulin domain

    7. XM_011536522.4 → XP_011534824.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X3

      Conserved Domains (3) summary
      cd00096
      Location:424 → 496
      Ig; Immunoglobulin domain
      smart00408
      Location:325 → 386
      IGc2; Immunoglobulin C-2 Type
      smart00410
      Location:117 → 197
      IG_like; Immunoglobulin like

    8. XM_047431051.1 → XP_047287007.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X5

    9. XM_017021061.3 → XP_016876550.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      41038514..41874449 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375504.1 → XP_054231479.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X1

    2. XM_054375505.1 → XP_054231480.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

    3. XM_054375506.1 → XP_054231481.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

    4. XM_054375507.1 → XP_054231482.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X2

    5. XM_054375509.1 → XP_054231484.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X4

    6. XM_054375512.1 → XP_054231487.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X7

    7. XM_054375508.1 → XP_054231483.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X3

    8. XM_054375510.1 → XP_054231485.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X5

    9. XM_054375511.1 → XP_054231486.1  MAM domain-containing glycosylphosphatidylinositol anchor protein 2 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z553.2 GenPept UniProtKB/Swiss-Prot:Q7Z553

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