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Aliases for CSMD3 Gene

Aliases for CSMD3 Gene

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

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 Benign Adult Familial Myoclonic Epilepsy and Trichorhinophalangeal Syndrome, Type Ii. An important paralog of this gene is CSMD1.

UniProtKB/Swiss-Prot for CSMD3 Gene

  • Involved in dendrite development.

Additional gene information for CSMD3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CSMD3 Gene

Genomics for CSMD3 Gene

GeneHancer (GH) Regulatory Elements for CSMD3 Gene

Promoters and enhancers for CSMD3 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
GH08J113437 Enhancer 0.7 ENCODE 650.7 -0.4 -400 0.2 ELF3 CTCF IRF2 MXI1 RB1 SIN3A CEBPG RAD21 RFX5 GATA3 CSMD3 GC08M113562
GH08J113438 Enhancer 0.7 Ensembl 650.7 -0.7 -734 0.4 ELF3 CTCF IRF2 MXI1 RB1 SIN3A CEBPG RAD21 RFX5 GATA3 CSMD3 GC08M113562
GH08J113436 Promoter 0.6 EPDnew 650.7 +0.5 508 0.1 POLR2A CSMD3 LOC105375709
GH08J113377 Promoter 0.5 EPDnew 661.1 +60.3 60312 0.1 CSMD3 RPL18P7 LOC105375709
GH08J113435 Enhancer 0.4 FANTOM5 654.6 +2.0 1972 0.4 MXI1 FOS CSMD3 LOC105375709
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for CSMD3 Gene

Genomic Locations for CSMD3 Gene
chr8:112,222,928-113,437,467
(GRCh38/hg38)
Size:
1,214,540 bases
Orientation:
Minus strand
chr8:113,235,157-114,449,328
(GRCh37/hg19)
Size:
1,214,172 bases
Orientation:
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:
    Q7Z407-CSMD3_HUMAN
    Recommended name:
    CUB and sushi domain-containing protein 3
    Protein Accession:
    Q7Z407
    Secondary Accessions:
    • Q96PZ3

    Protein attributes for CSMD3 Gene

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

    Alternative splice isoforms for CSMD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CSMD3 Gene

Post-translational modifications for CSMD3 Gene

  • Glycosylation at Asn3627, Asn3618, posLast=36123612, posLast=35293529, posLast=35223522, posLast=33643364, posLast=32763276, posLast=32183218, Asn3208, posLast=31943194, posLast=31673167, posLast=31583158, posLast=30993099, posLast=29522952, posLast=29322932, posLast=28622862, posLast=27422742, Asn2711, posLast=25372537, Asn2495, posLast=23242324, Asn2291, Asn2286, Asn2155, Asn2019, Asn1929, Asn1781, Asn1709, posLast=15911591, posLast=15361536, posLast=12801280, Asn1171, posLast=11261126, posLast=10921092, Asn966, posLast=823823, posLast=724724, Asn409, Asn361, posLast=9090, and Asn73
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CSMD3 Gene

Domains & Families for CSMD3 Gene

Gene Families for CSMD3 Gene

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

Suggested Antigen Peptide Sequences for CSMD3 Gene

Graphical View of Domain Structure for InterPro Entry

Q7Z407

UniProtKB/Swiss-Prot:

CSMD3_HUMAN :
  • The intracellular region is dispensable for its function.
  • Belongs to the CSMD family.
Domain:
  • The intracellular region is dispensable for its function.
Family:
  • 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 Model Products

  • Taconic Biosciences Mouse Models for CSMD3

miRNA for CSMD3 Gene

miRTarBase miRNAs that target CSMD3

Clone Products

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

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 CSMD3 gene
Compartment Confidence
plasma membrane 5

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

SuperPathways for CSMD3 Gene

No Data Available

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

Unigene Clusters for CSMD3 Gene

CUB and Sushi multiple domains 3:
Representative Sequences:

Clone Products

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: - - - -
SP4:
SP5:
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 ^
SP1:
SP2:
SP3:
SP4: - -
SP5:
SP6:

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: -
SP5:
SP6:

Relevant External Links for CSMD3 Gene

GeneLoc Exon Structure for
CSMD3
ECgene alternative splicing isoforms for
CSMD3

Expression for CSMD3 Gene

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

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

NURSA nuclear receptor signaling pathways regulating expression of CSMD3 Gene:

CSMD3

SOURCE GeneReport for Unigene cluster for CSMD3 Gene:

Hs.91381

mRNA Expression by UniProt/SwissProt for CSMD3 Gene:

Q7Z407-CSMD3_HUMAN
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(4.3)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with CSMD3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and 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
chimpanzee
(Pan troglodytes)
Mammalia CSMD3 34 33
  • 99.53 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CSMD3 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia CSMD3 34 33
  • 94.8 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CSMD3 34
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Csmd3 16 34 33
  • 91.14 (n)
rat
(Rattus norvegicus)
Mammalia Csmd3 33
  • 90.26 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CSMD3 34
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves CSMD3 34 33
  • 84.64 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CSMD3 34
  • 92 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii CSMD3 (1 of 3) 34
  • 81 (a)
OneToMany
CSMD3 (2 of 3) 34
  • 76 (a)
OneToMany
LOC572419 33
  • 72.17 (n)
CSMD3 (3 of 3) 34
  • 34 (a)
OneToMany
Species where no ortholog for CSMD3 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CSMD3 Gene

ENSEMBL:
Gene Tree for CSMD3 (if available)
TreeFam:
Gene Tree for CSMD3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CSMD3: view image

Paralogs for CSMD3 Gene

Paralogs for CSMD3 Gene

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

  • CSMD3_HUMAN
  • A5D6Y2_HUMAN
  • H7BXX0_HUMAN
  • L8EBH7_HUMAN
genes like me logo Genes that share paralogs with CSMD3: view

Variants for CSMD3 Gene

Sequence variations from dbSNP and Humsavar for CSMD3 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs139968762 A colorectal cancer sample 112,254,287(-) C/T coding_sequence_variant, missense_variant
rs780986269 A colorectal cancer sample 112,287,159(-) C/T coding_sequence_variant, missense_variant
VAR_035688 A colorectal cancer sample p.Trp322Gly
rs1000004478 -- 113,009,604(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000006375 -- 112,324,678(-) C/A intron_variant

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)
CSMD3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CSMD3

SNP Genotyping and Copy Number Assay Products

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

Disorders for CSMD3 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CSMD3 Gene - From: HGMD, DISEASES, and GeneCards

- 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

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  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 58
  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 44 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  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 58

Products for CSMD3 Gene

Sources for CSMD3 Gene

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