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Aliases for SYNDIG1 Gene

Aliases for SYNDIG1 Gene

  • Synapse Differentiation Inducing 1 2 3 5
  • Transmembrane Protein 90B 2 3 4
  • Interferon Induced Transmembrane Protein Domain Containing 5 2 3
  • Synapse Differentiation Induced Gene 1 2 3
  • Dispanin Subfamily C Member 2 3 4
  • C20orf39 3 4
  • TMEM90B 3 4
  • DSPC2 3 4
  • Synapse Differentiation-Inducing Gene Protein 1 3
  • Chromosome 20 Open Reading Frame 39 2
  • IFITMD5 3
  • SynDIG1 4

External Ids for SYNDIG1 Gene

Previous HGNC Symbols for SYNDIG1 Gene

  • C20orf39
  • TMEM90B

Summaries for SYNDIG1 Gene

Entrez Gene Summary for SYNDIG1 Gene

  • This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

GeneCards Summary for SYNDIG1 Gene

SYNDIG1 (Synapse Differentiation Inducing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and glutamate receptor binding. An important paralog of this gene is SYNDIG1L.

UniProtKB/Swiss-Prot for SYNDIG1 Gene

  • May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation.

Additional gene information for SYNDIG1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNDIG1 Gene

Genomics for SYNDIG1 Gene

GeneHancer (GH) Regulatory Elements for SYNDIG1 Gene

Promoters and enhancers for SYNDIG1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20I024468 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.4 392 1.4 ZNF777 ZNF76 SIN3A ZIC2 HIC1 ZNF335 E2F1 ZFHX2 GLIS2 ZNF143 GC20M024469 SYNDIG1 LOC105372585
GH20I024470 Enhancer 0.7 ENCODE dbSUPER 550.8 +1.4 1372 0 ZNF335 ZNF76 ZEB2 ZBTB26 EZH2 GC20M024469 SYNDIG1 LOC105372585
GH20I024471 Enhancer 0.6 FANTOM5 dbSUPER 556.9 +1.9 1947 0.2 SIN3A EZH2 SYNDIG1 LOC105372585
GH20I024431 Enhancer 0.5 ENCODE 10.2 -36.9 -36880 1 ZFHX2 GLIS1 HNF4G HNF4A EGR2 SYNDIG1 GAPDHP53 LOC105372577
GH20I024442 Enhancer 0.5 ENCODE 8.8 -25.5 -25528 2 SCRT1 SCRT2 POU5F1 CTBP2 GAPDHP53 SYNDIG1 LOC105372577
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SYNDIG1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for SYNDIG1 Gene

Genomic Locations for SYNDIG1 Gene
197,419 bases
Plus strand

Genomic View for SYNDIG1 Gene

Genes around SYNDIG1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYNDIG1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYNDIG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNDIG1 Gene

Proteins for SYNDIG1 Gene

  • Protein details for SYNDIG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Synapse differentiation-inducing gene protein 1
    Protein Accession:
    Secondary Accessions:
    • Q6IA30
    • Q9H514

    Protein attributes for SYNDIG1 Gene

    258 amino acids
    Molecular mass:
    28551 Da
    Quaternary structure:
    • Homodimer. Interacts with GRIA1 and GRIA2 (By similarity).

neXtProt entry for SYNDIG1 Gene

Post-translational modifications for SYNDIG1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SYNDIG1 Gene

Domains & Families for SYNDIG1 Gene

Gene Families for SYNDIG1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SYNDIG1 Gene


Suggested Antigen Peptide Sequences for SYNDIG1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the CD225/Dispanin family.
  • Belongs to the CD225/Dispanin family.
genes like me logo Genes that share domains with SYNDIG1: view

Function for SYNDIG1 Gene

Molecular function for SYNDIG1 Gene

UniProtKB/Swiss-Prot Function:
May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation.

Phenotypes From GWAS Catalog for SYNDIG1 Gene

Gene Ontology (GO) - Molecular Function for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0035254 glutamate receptor binding ISS,IEA --
GO:0042803 protein homodimerization activity ISS,IEA --
genes like me logo Genes that share ontologies with SYNDIG1: view

Phenotypes for SYNDIG1 Gene

GenomeRNAi human phenotypes for SYNDIG1:
genes like me logo Genes that share phenotypes with SYNDIG1: view

Animal Model Products

miRNA for SYNDIG1 Gene

miRTarBase miRNAs that target SYNDIG1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYNDIG1 Gene

Localization for SYNDIG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNDIG1 Gene

Cell membrane; Single-pass type II membrane protein. Early endosome membrane; Single-pass type II membrane protein. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Cell junction, synapse. Cell projection, dendrite. Cell projection, dendritic spine. Note=Shuttles between the cell surface and early endosome membrane. {ECO:0000250}.

Subcellular locations from

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 SYNDIG1 gene
Compartment Confidence
plasma membrane 5
endosome 4
peroxisome 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IEA,ISS --
GO:0014069 postsynaptic density ISS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SYNDIG1: view

Pathways & Interactions for SYNDIG1 Gene

SuperPathways for SYNDIG1 Gene

No Data Available

Interacting Proteins for SYNDIG1 Gene

Gene Ontology (GO) - Biological Process for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA,ISS --
GO:0009607 response to biotic stimulus IEA --
GO:0051965 positive regulation of synapse assembly IDA,IEA 20152115
GO:0097091 synaptic vesicle clustering ISS,IEA --
genes like me logo Genes that share ontologies with SYNDIG1: view

No data available for Pathways by source and SIGNOR curated interactions for SYNDIG1 Gene

Drugs & Compounds for SYNDIG1 Gene

No Compound Related Data Available

Transcripts for SYNDIG1 Gene

mRNA/cDNA for SYNDIG1 Gene

Unigene Clusters for SYNDIG1 Gene

Synapse differentiation inducing 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNDIG1 Gene

No ASD Table

Relevant External Links for SYNDIG1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYNDIG1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SYNDIG1 Gene

mRNA differential expression in normal tissues according to GTEx for SYNDIG1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x4.6), Brain - Cortex (x4.1), and Brain - Cerebellum (x4.0).

Protein differential expression in normal tissues from HIPED for SYNDIG1 Gene

This gene is overexpressed in Lung (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SYNDIG1 Gene

Protein tissue co-expression partners for SYNDIG1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SYNDIG1 Gene:


SOURCE GeneReport for Unigene cluster for SYNDIG1 Gene:


Evidence on tissue expression from TISSUES for SYNDIG1 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with SYNDIG1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYNDIG1 Gene

Orthologs for SYNDIG1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNDIG1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TMEM90B 34
  • 100 (a)
  • 99.74 (n)
(Monodelphis domestica)
Mammalia SYNDIG1 34
  • 98 (a)
(Canis familiaris)
Mammalia SYNDIG1 34
  • 94 (a)
TMEM90B 33
  • 90.57 (n)
(Rattus norvegicus)
Mammalia Syndig1 33
  • 87.98 (n)
(Mus musculus)
Mammalia Syndig1 33 16 34
  • 87.73 (n)
(Bos Taurus)
Mammalia SYNDIG1 33 34
  • 85.27 (n)
(Ornithorhynchus anatinus)
Mammalia SYNDIG1 34
  • 76 (a)
(Gallus gallus)
Aves SYNDIG1 33 34
  • 80.99 (n)
(Anolis carolinensis)
Reptilia SYNDIG1 34
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia syndig1 33
  • 74.68 (n)
(Danio rerio)
Actinopterygii LOC792553 33
  • 73.25 (n)
  • 63 (a)
Species where no ortholog for SYNDIG1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SYNDIG1 Gene

Gene Tree for SYNDIG1 (if available)
Gene Tree for SYNDIG1 (if available)

Paralogs for SYNDIG1 Gene

Paralogs for SYNDIG1 Gene

(1) SIMAP similar genes for SYNDIG1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SYNDIG1: view

Variants for SYNDIG1 Gene

Sequence variations from dbSNP and Humsavar for SYNDIG1 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs1000036657 -- 24,532,098(+) G/A intron_variant
rs1000039001 -- 24,652,900(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000044473 -- 24,595,787(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000065719 -- 24,572,995(+) G/C genic_downstream_transcript_variant, intron_variant
rs1000076817 -- 24,532,677(+) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SYNDIG1 Gene

Variant ID Type Subtype PubMed ID
nsv9793 CNV gain+loss 18304495
nsv833946 CNV gain 17160897
nsv524920 CNV gain 19592680
nsv522873 CNV gain 19592680
nsv513540 CNV insertion 21212237
nsv179076 CNV deletion 16902084
nsv178771 CNV deletion 16902084
nsv1115598 CNV duplication 24896259
esv990034 CNV loss 20482838
esv3645555 CNV loss 21293372
esv3645554 CNV loss 21293372
esv3645553 CNV gain 21293372
esv3645552 CNV gain 21293372
esv3645551 CNV loss 21293372
esv3567927 CNV loss 25503493
esv3567926 CNV loss 25503493
esv3378968 CNV insertion 20981092
esv2673324 CNV deletion 23128226
esv2662588 CNV deletion 23128226
esv2657114 CNV deletion 23128226
esv2651577 CNV insertion 19546169
esv2540968 CNV insertion 19546169
esv1529124 CNV insertion 17803354

Variation tolerance for SYNDIG1 Gene

Residual Variation Intolerance Score: 66.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.90; 35.36% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYNDIG1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNDIG1 Gene

Disorders for SYNDIG1 Gene

Additional Disease Information for SYNDIG1

No disorders were found for SYNDIG1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYNDIG1 Gene

Publications for SYNDIG1 Gene

  1. The dispanins: a novel gene family of ancient origin that contains 14 human members. (PMID: 22363774) Sällman Almén M … Schiöth HB (PloS one 2012) 3 4 58
  2. SynDIG1: an activity-regulated, AMPA- receptor-interacting transmembrane protein that regulates excitatory synapse development. (PMID: 20152115) Kalashnikova E … Díaz E (Neuron 2010) 2 3 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4 58

Products for SYNDIG1 Gene

Sources for SYNDIG1 Gene

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