Aliases for CSMD3 Gene

Aliases for CSMD3 Gene

  • CUB And Sushi Multiple Domains 3 2 3 5
  • CUB And Sushi Domain-Containing Protein 3 3 4
  • CUB And Sushi Multiple Domains Protein 3 3 4
  • KIAA1894 4
  • CSMD3 5

External Ids for CSMD3 Gene

Previous GeneCards Identifiers for CSMD3 Gene

  • GC00U903104
  • GC08M112903
  • GC08M113191
  • GC08M113304
  • GC08M108554

Summaries for CSMD3 Gene

GeneCards Summary for CSMD3 Gene

CSMD3 (CUB And Sushi Multiple Domains 3) is a Protein Coding gene. Diseases associated with CSMD3 include Familial Adult Myoclonic Epilepsy and Trichorhinophalangeal Syndrome, Type Ii. An important paralog of this gene is CSMD1.

UniProtKB/Swiss-Prot Summary for CSMD3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CSMD3 Gene

Genomics for CSMD3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CSMD3 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
GH08J113434 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 254.5 +0.9 898 4.4 ZNF654 CEBPA CEBPB REST DEK TRIM22 CTCF ZNF217 SIN3A RAD21 CSMD3 ENSG00000286937 HSALNG0067817-001 lnc-TRPS1-4 ENSG00000287819
GH08J113377 Promoter 0.3 EPDnew 261.1 +60.3 60344 0.1 CSMD3 ENSG00000227514 RPL18P7 LOC105375709 lnc-TRPS1-4
GH08J112805 Enhancer 0.6 Ensembl ENCODE 11.5 +630.6 630598 3.4 RAD21 SMC3 CTCF ZNF652 GATA2 CSMD3 HSALNG0067811 piR-50968-131
GH08J113409 Enhancer 0.2 FANTOM5 13.9 +27.5 27535 0.2 CSMD3 LOC105375709 lnc-TRPS1-4 ENSG00000227514
GH08J113433 Enhancer 0.2 FANTOM5 10.8 +4.1 4084 0.2 ENSG00000287819 LOC105375709 CSMD3 lnc-TRPS1-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSMD3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CSMD3

Top Transcription factor binding sites by QIAGEN in the CSMD3 gene promoter:
  • CUTL1
  • FAC1
  • FOXL1
  • IRF-7A
  • Nkx2-2
  • Pax-3
  • POU2F1
  • POU2F1a
  • S8
  • STAT5A

Genomic Locations for CSMD3 Gene

Latest Assembly
1,214,572 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
1,214,012 bases
Minus strand

(GRCh37/hg19 by Ensembl)
1,214,172 bases
Minus strand

Genomic View for CSMD3 Gene

Genes around CSMD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CSMD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CSMD3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CSMD3 Gene

Proteins for CSMD3 Gene

  • Protein details for CSMD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CUB and sushi domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q96PZ3

    Protein attributes for CSMD3 Gene

    3707 amino acids
    Molecular mass:
    406000 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAO34702.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CSMD3 Gene


neXtProt entry for CSMD3 Gene

Post-translational modifications for CSMD3 Gene

  • Glycosylation at Asn73, Asn90, Asn361, Asn409, Asn724, Asn823, Asn966, Asn1092, Asn1126, Asn1171, Asn1280, Asn1536, Asn1591, Asn1709, Asn1781, Asn1929, Asn2019, Asn2155, Asn2286, Asn2291, Asn2324, Asn2495, Asn2537, Asn2711, Asn2742, Asn2862, Asn2932, Asn2952, Asn3099, Asn3158, Asn3167, Asn3194, Asn3208, Asn3218, Asn3276, Asn3364, Asn3522, Asn3529, Asn3612, Asn3618, and Asn3627
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CSMD3 Gene

Domains & Families for CSMD3 Gene

Gene Families for CSMD3 Gene

Protein Domains for CSMD3 Gene

  • CUB domain
  • Sushi domain/SCR domain/CCP module

Suggested Antigen Peptide Sequences for CSMD3 Gene

GenScript: Design optimal peptide antigens:
  • CSMD3 protein (A5D6Y2_HUMAN)
  • CUB and sushi multiple domains protein 3 (CSMD3_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • The intracellular region is dispensable for its function.
  • Belongs to the CSMD family.
  • The intracellular region is dispensable for its function.
  • Belongs to the CSMD family.
genes like me logo Genes that share domains with CSMD3: view

Function for CSMD3 Gene

Molecular function for CSMD3 Gene

UniProtKB/Swiss-Prot Function:
Involved in dendrite development.

Phenotypes From GWAS Catalog for CSMD3 Gene

genes like me logo Genes that share phenotypes with CSMD3: view

Animal Models for research

  • Taconic Biosciences Mouse Models for CSMD3

miRNA for CSMD3 Gene

miRTarBase miRNAs that target CSMD3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CSMD3

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CSMD3 Gene

Localization for CSMD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSMD3 Gene

Cell membrane. Multi-pass membrane protein.

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 CSMD3 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
nucleus 1

Gene Ontology (GO) - Cellular Components for CSMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane ISS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CSMD3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CSMD3 Gene

Pathways & Interactions for CSMD3 Gene

PathCards logo

SuperPathways for CSMD3 Gene

No Data Available

Interacting Proteins for CSMD3 Gene

Gene Ontology (GO) - Biological Process for CSMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0050773 regulation of dendrite development ISS --
genes like me logo Genes that share ontologies with CSMD3: view

No data available for Pathways by source and SIGNOR curated interactions for CSMD3 Gene

Drugs & Compounds for CSMD3 Gene

No Compound Related Data Available

Transcripts for CSMD3 Gene

mRNA/cDNA for CSMD3 Gene

8 NCBI additional mRNA sequence :
10 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 CSMD3

Alternative Splicing Database (ASD) splice patterns (SP) for CSMD3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2: - - -
SP3: - - - -
SP6: - -

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45a · 45b ^ 46 ^ 47 ^
SP4: - -

ExUns: 48 ^ 49 ^ 50 ^ 51 ^ 52a · 52b ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60 ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67 ^ 68 ^ 69 ^ 70 ^ 71 ^ 72
SP1: -
SP2: -
SP3: - -
SP4: -

Relevant External Links for CSMD3 Gene

GeneLoc Exon Structure for

Expression for CSMD3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CSMD3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CSMD3 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.8), Brain - Hypothalamus (x5.5), Brain - Anterior cingulate cortex (BA24) (x5.0), Brain - Frontal Cortex (BA9) (x4.8), Brain - Amygdala (x4.4), and Brain - Cortex (x4.2).

Protein differential expression in normal tissues from HIPED for CSMD3 Gene

This gene is overexpressed in Pancreatic juice (45.1) and Urine (23.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CSMD3 Gene

Protein tissue co-expression partners for CSMD3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CSMD3

SOURCE GeneReport for Unigene cluster for CSMD3 Gene:


mRNA Expression by UniProt/SwissProt for CSMD3 Gene:

Tissue specificity: Weakly expressed in most tissues, except in brain. Expressed at intermediate level in brain, including cerebellum, substantia nigra, thalamus, spinal cord, hippocampus and fetal brain. Also expressed in testis.

Evidence on tissue expression from TISSUES for CSMD3 Gene

  • Nervous system(4.5)
  • Liver(4.3)
genes like me logo Genes that share expression patterns with CSMD3: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CSMD3 Gene

Orthologs for CSMD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CSMD3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CSMD3 29 30
  • 99.53 (n)
(Monodelphis domestica)
Mammalia CSMD3 30
  • 97 (a)
(Canis familiaris)
Mammalia CSMD3 29 30
  • 94.8 (n)
(Bos Taurus)
Mammalia CSMD3 30
  • 93 (a)
(Mus musculus)
Mammalia Csmd3 29 16 30
  • 91.14 (n)
(Rattus norvegicus)
Mammalia Csmd3 29
  • 90.26 (n)
(Ornithorhynchus anatinus)
Mammalia CSMD3 30
  • 67 (a)
(Gallus gallus)
Aves CSMD3 29 30
  • 84.64 (n)
(Anolis carolinensis)
Reptilia CSMD3 30
  • 92 (a)
(Danio rerio)
Actinopterygii CSMD3 (1 of 3) 30
  • 81 (a)
CSMD3 (2 of 3) 30
  • 76 (a)
LOC572419 29
  • 72.17 (n)
CSMD3 (3 of 3) 30
  • 34 (a)
Species where no ortholog for CSMD3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CSMD3 Gene

Gene Tree for CSMD3 (if available)
Gene Tree for CSMD3 (if available)
Evolutionary constrained regions (ECRs) for CSMD3: view image
Alliance of Genome Resources:
Additional Orthologs for CSMD3

Paralogs for CSMD3 Gene

(9) SIMAP similar genes for CSMD3 Gene using alignment to 4 proteins:

  • A5D6Y2_HUMAN
genes like me logo Genes that share paralogs with CSMD3: view

Variants for CSMD3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CSMD3 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
972956 Not Provided: not provided 113,314,705(-) T/C
NM_198123.2(CSMD3):c.267A>G (p.Ala89=)
rs10955625 Benign: not provided 112,503,980(-) G/A
rs113972313 Benign: not provided 112,975,949(-) C/A
NM_198123.2(CSMD3):c.1230G>T (p.Thr410=)
rs114926522 Likely Benign: not provided 112,291,619(-) G/A
NM_198123.2(CSMD3):c.8865C>T (p.Tyr2955=)
rs115208768 Benign: not provided 112,263,769(-) C/A
NM_198123.2(CSMD3):c.9732G>T (p.Leu3244=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CSMD3 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 CSMD3 Gene

Variant ID Type Subtype PubMed ID
dgv12265n54 CNV loss 21841781
dgv12266n54 CNV loss 21841781
dgv12267n54 CNV loss 21841781
dgv12268n54 CNV loss 21841781
dgv12269n54 CNV loss 21841781
dgv12270n54 CNV loss 21841781
dgv12271n54 CNV loss 21841781
dgv12272n54 CNV loss 21841781
dgv187e180 CNV deletion 20482838
dgv188e180 CNV loss 20482838
dgv2108e212 CNV loss 25503493
dgv7285n100 CNV loss 25217958
dgv7286n100 CNV loss 25217958
dgv7287n100 CNV loss 25217958
esv25527 CNV loss 19812545
esv2660416 CNV deletion 23128226
esv2666384 CNV deletion 23128226
esv2670906 CNV deletion 23128226
esv2674135 CNV deletion 23128226
esv2761461 CNV gain 21179565
esv28758 CNV loss 19812545
esv3270718 CNV deletion 24192839
esv3398405 CNV insertion 20981092
esv3425186 CNV insertion 20981092
esv3544026 CNV deletion 23714750
esv3544027 CNV deletion 23714750
esv3572934 CNV loss 25503493
esv3572935 CNV loss 25503493
esv3572936 CNV loss 25503493
esv3572937 CNV loss 25503493
esv3572940 CNV loss 25503493
esv3572941 CNV loss 25503493
esv3618455 CNV loss 21293372
esv3618459 CNV loss 21293372
esv3618461 CNV loss 21293372
esv3618462 CNV loss 21293372
esv3618463 CNV loss 21293372
esv3618464 CNV loss 21293372
esv3618465 CNV loss 21293372
esv3618466 CNV loss 21293372
esv3618467 CNV loss 21293372
nsv1017791 CNV loss 25217958
nsv1019197 CNV gain 25217958
nsv1027156 CNV gain 25217958
nsv1030305 CNV loss 25217958
nsv1034285 CNV loss 25217958
nsv1124367 CNV deletion 24896259
nsv1140388 OTHER inversion 24896259
nsv1153182 CNV duplication 26484159
nsv465766 CNV loss 19166990
nsv476092 CNV novel sequence insertion 20440878
nsv476645 CNV novel sequence insertion 20440878
nsv478922 CNV novel sequence insertion 20440878
nsv507482 OTHER sequence alteration 20534489
nsv511390 CNV loss 21212237
nsv511403 CNV loss 21212237
nsv512060 CNV loss 21212237
nsv512061 CNV loss 21212237
nsv518270 CNV loss 19592680
nsv524089 CNV gain 19592680
nsv611908 CNV loss 21841781
nsv611909 CNV loss 21841781
nsv6352 CNV insertion 18451855
nsv831427 CNV loss 17160897
nsv831428 CNV gain 17160897
nsv831429 CNV loss 17160897
nsv957654 CNV deletion 24416366

Variation tolerance for CSMD3 Gene

Residual Variation Intolerance Score: 0.133% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.94; 95.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CSMD3 Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CSMD3 Gene

Disorders for CSMD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CSMD3 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search CSMD3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CSMD3

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CSMD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CSMD3 Gene

Publications for CSMD3 Gene

  1. Identification of two new members of the CSMD gene family. (PMID: 12906867) Lau WL … Scholnick SB (Genomics 2003) 3 4 22
  2. A novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains: a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1. (PMID: 12943675) Shimizu A … Shimizu N (Biochemical and biophysical research communications 2003) 3 4 22
  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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4

Products for CSMD3 Gene

Sources for CSMD3 Gene