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 mamm... See more...

Aliases for MDGA1 Gene

Aliases for MDGA1 Gene

  • MAM Domain Containing Glycosylphosphatidylinositol Anchor 1 2 3 5
  • MAMDC3 2 3 4
  • GPIM 2 3 4
  • MAM Domain-Containing Glycosylphosphatidylinositol Anchor Protein 1 3 4
  • Glycosylphosphatidylinositol-MAM 3 4
  • MAM Domain-Containing Protein 3 3 4
  • GPI And MAM Protein 3 4
  • MDGA1 5

External Ids for MDGA1 Gene

Previous GeneCards Identifiers for MDGA1 Gene

  • GC06U990326
  • GC06M037596
  • GC06M037647
  • GC06M037708
  • GC06M037319
  • GC06M037598
  • GC06M038976
  • GC06M039795
  • GC06M039973
  • GC06M041310
  • GC06M037739
  • GC06M037752
  • GC06M038090
  • GC06M038479
  • GC06M038826
  • GC06M042236
  • GC06M043496

Summaries for MDGA1 Gene

Entrez Gene Summary for MDGA1 Gene

  • 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]

GeneCards Summary for MDGA1 Gene

MDGA1 (MAM Domain Containing Glycosylphosphatidylinositol Anchor 1) is a Protein Coding gene. Diseases associated with MDGA1 include Bipolar Disorder and Ovarian Lymphoma. Among its related pathways are Post-translational modification- synthesis of GPI-anchored proteins and Metabolism of proteins. An important paralog of this gene is MDGA2.

UniProtKB/Swiss-Prot Summary for MDGA1 Gene

  • Required for radial migration of cortical neurons in the superficial layer of the neocortex (By similarity). Plays a role in the formation or maintenance of inhibitory synapses. May function by inhibiting the activity of NLGN2.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for MDGA1 Gene

Genomics for MDGA1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for MDGA1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J037695 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 329.3 +1.8 1800 4.2 EZH2 NCOR1 ZNF600 IKZF1 ZBTB10 NONO ZNF341 MNT KLF7 SIN3A MDGA1 HSALNG0049834 TBC1D22B HSALNG0049833 CCDC167
GH06J037704 Promoter/Enhancer 1.8 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 70.9 -6.3 -6320 2 ZNF654 MYC POLR2A ZIC2 ZBTB10 REST ZNF592 TRIM22 ZNF341 MNT lnc-ZFAND3-6 MDGA1 TBC1D22B NONHSAG043702.2 HSALNG0049836 ZFAND3
GH06J037638 Enhancer 0.8 Ensembl 61.6 +60.5 60505 1.2 IKZF1 ZNF592 ZIC2 REST ZNF316 NFE2 JUND MYNN MAFK SMARCA4 MDGA1 lnc-CCDC167-2 HSALNG0049826 CCDC167
GH06J037628 Enhancer 1 Ensembl ENCODE 46.6 +69.3 69305 4.4 NCOR1 IKZF1 JUND NFIC ZIC2 CEBPB ELK1 MAX EP300 ELF1 MDGA1 HSALNG0049826 lnc-CCDC167-2 CCDC167
GH06J037648 Promoter/Enhancer 0.9 Ensembl ENCODE 34.2 +50.5 50517 1.2 SP2 TAF1 NRF1 L3MBTL2 EGR1 KLF1 USF2 POLR2A KLF8 BACH1 HSALNG0049829 lnc-CCDC167-3 MDGA1 RNF8 HSALNG0049831 CCDC167
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around MDGA1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for MDGA1

Top Transcription factor binding sites by QIAGEN in the MDGA1 gene promoter:
  • AP-4
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • Elk-1
  • MAZR
  • USF1

Genomic Locations for MDGA1 Gene

Latest Assembly
chr6:37,630,679-37,699,306
(GRCh38/hg38)
Size:
68,628 bases
Orientation:
Minus strand

Previous Assembly
chr6:37,598,455-37,665,659
(GRCh37/hg19 by Entrez Gene)
Size:
67,205 bases
Orientation:
Minus strand

chr6:37,600,284-37,667,082
(GRCh37/hg19 by Ensembl)
Size:
66,799 bases
Orientation:
Minus strand

Genomic View for MDGA1 Gene

Genes around MDGA1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
MDGA1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for MDGA1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for MDGA1 Gene

Proteins for MDGA1 Gene

  • Protein details for MDGA1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NFP4-MDGA1_HUMAN
    Recommended name:
    MAM domain-containing glycosylphosphatidylinositol anchor protein 1
    Protein Accession:
    Q8NFP4
    Secondary Accessions:
    • A6NHG0
    • Q8NBE3

    Protein attributes for MDGA1 Gene

    Size:
    955 amino acids
    Molecular mass:
    105790 Da
    Quaternary structure:
    • Interacts heterophilically through its MAM domain with proteins in axon-rich regions and through its Ig-like domains with proteins in differentiating muscle (By similarity). Interacts (through the Ig-like domains) with NLGN2.
    SequenceCaution:
    • Sequence=BAC03502.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for MDGA1 Gene

    Alternative splice isoforms for MDGA1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for MDGA1 Gene

Post-translational modifications for MDGA1 Gene

  • Glycosylation at Asn42, Asn90, Asn235, Asn247, Asn257, Asn307, Asn331, Asn432, Asn655, Asn747, and Asn826
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for MDGA1 Gene

Domains & Families for MDGA1 Gene

Gene Families for MDGA1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for MDGA1 Gene

InterPro:
Blocks:
  • Immunoglobulin C-2 type
  • Immunoglobulin subtype
  • MAM domain signature

Suggested Antigen Peptide Sequences for MDGA1 Gene

GenScript: Design optimal peptide antigens:
  • MAM domain-containing protein 3 (MDGA1_HUMAN)
  • MAM domain containing glycosylphosphatidylinositol anchor 1 (Q5TFS7_HUMAN)
  • MAM domain containing glycosylphosphatidylinositol anchor 1 (Q5TFS8_HUMAN)
genes like me logo Genes that share domains with MDGA1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for MDGA1 Gene

Function for MDGA1 Gene

Molecular function for MDGA1 Gene

UniProtKB/Swiss-Prot Function:
Required for radial migration of cortical neurons in the superficial layer of the neocortex (By similarity). Plays a role in the formation or maintenance of inhibitory synapses. May function by inhibiting the activity of NLGN2.

Phenotypes From GWAS Catalog for MDGA1 Gene

Gene Ontology (GO) - Molecular Function for MDGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with MDGA1: view
genes like me logo Genes that share phenotypes with MDGA1: view

Animal Models for MDGA1 Gene

MGI Knock Outs for MDGA1:

Animal Models for research

  • Taconic Biosciences Mouse Models for MDGA1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MDGA1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for MDGA1 Gene

Localization for MDGA1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for MDGA1 Gene

Cell membrane. Lipid-anchor, GPI-anchor. Note=Associated with lipid rafts.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for MDGA1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
golgi apparatus 4
cytoskeleton 1
nucleus 1
peroxisome 0
cytosol 0
lysosome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for MDGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space HDA 22664934
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with MDGA1: view

Pathways & Interactions for MDGA1 Gene

genes like me logo Genes that share pathways with MDGA1: view

Interacting Proteins for MDGA1 Gene

Gene Ontology (GO) - Biological Process for MDGA1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001764 neuron migration ISS --
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
GO:0007420 brain development ISS 15019943
GO:0021527 spinal cord association neuron differentiation ISS 15019943
genes like me logo Genes that share ontologies with MDGA1: view

No data available for SIGNOR curated interactions for MDGA1 Gene

Drugs & Compounds for MDGA1 Gene

No Compound Related Data Available

Transcripts for MDGA1 Gene

mRNA/cDNA for MDGA1 Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for MDGA1

Alternative Splicing Database (ASD) splice patterns (SP) for MDGA1 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a ·
SP1:
SP2: - -
SP3: -
SP4:
SP5:
SP6: - -
SP7: -
SP8: -
SP9:
SP10:
SP11: -
SP12: -

ExUns: 18b · 18c ^ 19 ^ 20a · 20b · 20c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for MDGA1 Gene

GeneLoc Exon Structure for
MDGA1

Expression for MDGA1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for MDGA1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for MDGA1 Gene

This gene is overexpressed in Brain - Cerebellum (x19.2) and Brain - Cerebellar Hemisphere (x16.8).

Protein differential expression in normal tissues from HIPED for MDGA1 Gene

This gene is overexpressed in Fetal Brain (56.4) and Retina (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for MDGA1 Gene



Protein tissue co-expression partners for MDGA1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for MDGA1

SOURCE GeneReport for Unigene cluster for MDGA1 Gene:

Hs.437993

mRNA Expression by UniProt/SwissProt for MDGA1 Gene:

Q8NFP4-MDGA1_HUMAN
Tissue specificity: Has been found in brain, heart, skeletal muscle and kidney. Found to be overexpressed in tumor tissues.

Evidence on tissue expression from TISSUES for MDGA1 Gene

  • Adrenal gland(5)
  • Nervous system(4.8)
  • Bone marrow(4)
genes like me logo Genes that share expression patterns with MDGA1: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for MDGA1 Gene

Orthologs for MDGA1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for MDGA1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia MDGA1 29 30
  • 99.72 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia MDGA1 29 30
  • 92.42 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia MDGA1 29 30
  • 92.36 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Mdga1 29 16 30
  • 89.83 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Mdga1 29
  • 89.38 (n)
Oppossum
(Monodelphis domestica)
Mammalia MDGA1 30
  • 78 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia MDGA1 30
  • 63 (a)
OneToOne
Chicken
(Gallus gallus)
Aves MDGA1 29 30
  • 74.53 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia MDGA1 30
  • 76 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.13549 29
Zebrafish
(Danio rerio)
Actinopterygii LOC569180 29
  • 65.07 (n)
MDGA1 30
  • 61 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 33 (a)
OneToMany
Species where no ortholog for MDGA1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for MDGA1 Gene

ENSEMBL:
Gene Tree for MDGA1 (if available)
TreeFam:
Gene Tree for MDGA1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for MDGA1: view image
Alliance of Genome Resources:
Additional Orthologs for MDGA1

Paralogs for MDGA1 Gene

Paralogs for MDGA1 Gene

(8) SIMAP similar genes for MDGA1 Gene using alignment to 7 proteins:

  • MDGA1_HUMAN
  • D6RFG6_HUMAN
  • D6RHU8_HUMAN
  • H0Y4Q2_HUMAN
  • H0YA23_HUMAN
  • J3KNB7_HUMAN
  • L8EAS0_HUMAN
genes like me logo Genes that share paralogs with MDGA1: view

Variants for MDGA1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for MDGA1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs192113659 Benign: not provided 37,646,268(-) C/G
NM_153487.4(MDGA1):c.2154G>C (p.Glu718Asp)
MISSENSE
rs201158201 Benign: not provided 37,638,287(-) C/A
NM_153487.4(MDGA1):c.2694G>T (p.Pro898=)
SYNONYMOUS
rs74703632 Benign: not provided 37,638,260(-) A/G
NM_153487.4(MDGA1):c.2721T>C (p.Asp907=)
SYNONYMOUS
rs804815 Benign: not provided 37,650,116(-) G/A
NM_153487.4(MDGA1):c.1602C>T (p.Asn534=)
SYNONYMOUS
rs864309493 Uncertain Significance: Acute megakaryoblastic leukemia; Mediastinal germ cell tumor 37,638,307(-) A/C
NM_153487.4(MDGA1):c.2674T>G (p.Phe892Val)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for MDGA1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for MDGA1 Gene

Variant ID Type Subtype PubMed ID
esv2667581 CNV deletion 23128226
esv2731934 CNV deletion 23290073
esv2752124 CNV gain 17911159
esv27953 CNV loss 19812545
nsv1015689 CNV gain 25217958
nsv958351 CNV deletion 24416366

Variation tolerance for MDGA1 Gene

Residual Variation Intolerance Score: 18.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.35; 76.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for MDGA1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
MDGA1
Leiden Open Variation Database (LOVD)
MDGA1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for MDGA1 Gene

Disorders for MDGA1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for MDGA1 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
bipolar disorder
  • bipolar depression
ovarian lymphoma
schizophrenia
  • sczd
multiple personality disorder
  • dissociative identity disorder
- elite association - COSMIC cancer census association via MalaCards
Search MDGA1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for MDGA1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with MDGA1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for MDGA1 Gene

Publications for MDGA1 Gene

  1. Characterization of MDGA1, a novel human glycosylphosphatidylinositol-anchored protein localized in lipid rafts. (PMID: 15922729) Díaz-López A … De Juan C (Experimental cell research 2005) 2 3 4
  2. MDGAs interact selectively with neuroligin-2 but not other neuroligins to regulate inhibitory synapse development. (PMID: 23248271) Lee K … Ko J (Proceedings of the National Academy of Sciences of the United States of America 2013) 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 40
  4. WITHDRAWN: Common polymorphisms in the MDGA1 gene are associated with bipolar disorder and schizophrenia in the Chinese Han population. (PMID: 20036297) Li J … Shi Y (Progress in neuro-psychopharmacology & biological psychiatry 2009) 3 40
  5. Association analysis of schizophrenia on 18 genes involved in neuronal migration: MDGA1 as a new susceptibility gene. (PMID: 18384059) Kähler AK … Andreassen OA (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2008) 3 40

Products for MDGA1 Gene

Sources for MDGA1 Gene