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CSMD3 CUB and Sushi multiple domains 3 [ Homo sapiens (human) ]

Gene ID: 114788, updated on 3-Apr-2024

Summary

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Official Symbol
CSMD3provided by HGNC
Official Full Name
CUB and Sushi multiple domains 3provided by HGNC
Primary source
HGNC:HGNC:19291
See related
Ensembl:ENSG00000164796 MIM:608399; AllianceGenome:HGNC:19291
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
Summary
Predicted to be involved in regulation of dendrite development. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 1.9), testis (RPKM 0.7) and 1 other tissue See more
Orthologs
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Genomic context

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See CSMD3 in Genome Data Viewer
Location:
8q23.3
Exon count:
74
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (112222928..113436939, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (113347915..114561864, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (113235157..114449168, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375707 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:112928926-112929652 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:113206999-113207584 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:113230017-113230753 Neighboring gene RNA, U4 small nuclear 37, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr8:113479947-113480134 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:113606539-113607126 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:113685670-113686869 Neighboring gene ribosomal protein L30 pseudogene 16 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:113784503-113785202 Neighboring gene microRNA 2053 Neighboring gene uncharacterized LOC107986966 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:114444309-114445508 Neighboring gene uncharacterized LOC105375709 Neighboring gene NANOG hESC enhancer GRCh37_chr8:114447752-114448262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:114450102-114450602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:114536695-114537196 Neighboring gene ribosomal protein L18 pseudogene 7 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr8:114992841-114993557 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:115017837-115018380 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:115253724-115254490 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:115258898-115259836 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:115289230-115289421 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr8:115293734-115294656 Neighboring gene uncharacterized LOC105375710 Neighboring gene Sharpr-MPRA regulatory region 9676 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 7 pseudogene

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
  • 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. Association of chromosome 8q variants with prostate cancer risk in Caucasian and Hispanic men. Beuten J, et al. Carcinogenesis, 2009 Aug. PMID 19528667, Free PMC Article
  2. Two patients with balanced translocations and autistic disorder: CSMD3 as a candidate gene for autism found in their common 8q23 breakpoint area. Floris C, et al. Eur J Hum Genet, 2008 Jun. PMID 18270536
  3. Pronounced short stature in a girl with tricho-rhino-phalangeal syndrome II (TRPS II, Langer-Giedion syndrome) and growth hormone deficiency. Riedl S, et al. Am J Med Genet A, 2004 Dec 1. PMID 15523607
  4. Somatic mutations and germline sequence variants in patients with familial colorectal cancer. Gylfe AE, et al. Int J Cancer, 2010 Dec 15. PMID 21351276
  5. 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. Shimizu A, et al. Biochem Biophys Res Commun, 2003 Sep 12. PMID 12943675

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Nonsynonymous variants of CSMD3 is associated with familial colorectal cancer.
    Title: Somatic mutations and germline sequence variants in patients with familial colorectal cancer.
  2. 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.
  3. Single-nucleotide polymorphisms in CSMD3 is associated with prostate cancer risk in hispanic men.
    Title: Association of chromosome 8q variants with prostate cancer risk in Caucasian and Hispanic men.
  4. Breakpoints on chromosomes 8 in both patients do not interrupt any known gene but both map in a region containing the CSMD3 gene, which thereby can be considered as a candidate for autistic spectrum disorders
    Title: Two patients with balanced translocations and autistic disorder: CSMD3 as a candidate gene for autism found in their common 8q23 breakpoint area.
  5. CSMD3 encodes a protein with CUB and sushi multiple domains and is a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1
    Title: 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.
  6. CSMD3 is deleted in a subject with combined tricho-rhino-phalangeal syndrome II with mental retardation and growth hormone deficiency.
    Title: Pronounced short stature in a girl with tricho-rhino-phalangeal syndrome II (TRPS II, Langer-Giedion syndrome) and growth hormone deficiency.
  7. CSMD3 protein domain structure and the sequence of the cytoplasmic tail are highly conserved between mammals and fish.
    Title: Identification of two new members of the CSMD gene family.
Submit: New GeneRIF Correction

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
A genome-wide association study (GWAS) for bronchopulmonary dysplasia.
EBI GWAS Catalog
A genome-wide meta-analysis of association studies of Cloninger's Temperament Scales.
EBI GWAS Catalog
Genome-wide association study of periodontal pathogen colonization.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1894

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in regulation of dendrite development ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
CUB and sushi domain-containing protein 3
Names
CUB and sushi multiple domains protein 3

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_001363185.1 → NP_001350114.1  CUB and sushi domain-containing protein 3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AB067481, AB114604, AB114605, AY210419
    UniProtKB/TrEMBL
    H7BXX0
    Related
    ENSP00000341558.3, ENST00000339701.7
    Conserved Domains (5) summary
    cd00033
    Location:534 → 588
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00032
    Location:880 → 933
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    cd00041
    Location:1458 → 1565
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:1398 → 1454
    Sushi; Sushi repeat (SCR repeat)
    cl27761
    Location:2968 → 3207
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system

  2. NM_052900.3 → NP_443132.3  CUB and sushi domain-containing protein 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (c) differs in the 5' UTR and 5' coding region, compared to variant a. The resulting isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB114604, AB114605, AY210419
    Consensus CDS
    CCDS6316.2
    UniProtKB/TrEMBL
    H7BXX0
    Related
    ENSP00000412263.2, ENST00000455883.2
    Conserved Domains (5) summary
    cd00033
    Location:2648 → 2702
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00032
    Location:906 → 959
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:2999 → 3238
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:1484 → 1591
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:3064 → 3117
    Sushi; Sushi repeat (SCR repeat)

  3. NM_198123.2 → NP_937756.1  CUB and sushi domain-containing protein 3 isoform 1

    See identical proteins and their annotated locations for NP_937756.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (a) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB114604, AB114605, AY210419
    Consensus CDS
    CCDS6315.1
    UniProtKB/Swiss-Prot
    Q7Z407, Q96PZ3
    UniProtKB/TrEMBL
    H7BXX0
    Related
    ENSP00000297405.5, ENST00000297405.10
    Conserved Domains (5) summary
    cd00033
    Location:2817 → 2871
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00032
    Location:1010 → 1063
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:3168 → 3407
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:1588 → 1695
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:3233 → 3286
    Sushi; Sushi repeat (SCR repeat)

  4. NM_198124.2 → NP_937757.1  CUB and sushi domain-containing protein 3 isoform 2

    See identical proteins and their annotated locations for NP_937757.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (b) lacks two alternate in-frame exons in the mid coding region, compared to variant a. The resulting isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AB114605, AY210419
    Consensus CDS
    CCDS6317.1
    UniProtKB/TrEMBL
    H7BXX0
    Related
    ENSP00000345799.3, ENST00000343508.7
    Conserved Domains (5) summary
    cd00033
    Location:2777 → 2831
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00032
    Location:970 → 1023
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:3128 → 3367
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:1548 → 1655
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:3193 → 3246
    Sushi; Sushi repeat (SCR repeat)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    112222928..113436939 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013010.2 → XP_016868499.1  CUB and sushi domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    H7BXX0

  2. XM_011516816.3 → XP_011515118.1  CUB and sushi domain-containing protein 3 isoform X4

    UniProtKB/TrEMBL
    H7BXX0
    Conserved Domains (5) summary
    cd00033
    Location:2713 → 2767
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    smart00032
    Location:906 → 959
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:3064 → 3303
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:1484 → 1591
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:3129 → 3182
    Sushi; Sushi repeat (SCR repeat)

  3. XM_047421314.1 → XP_047277270.1  CUB and sushi domain-containing protein 3 isoform X3

  4. XM_017013008.2 → XP_016868497.1  CUB and sushi domain-containing protein 3 isoform X1

    UniProtKB/TrEMBL
    H7BXX0

  5. XM_017013009.3 → XP_016868498.1  CUB and sushi domain-containing protein 3 isoform X2

    UniProtKB/TrEMBL
    H7BXX0

  6. XM_011516815.3 → XP_011515117.1  CUB and sushi domain-containing protein 3 isoform X6

    Conserved Domains (4) summary
    cd00033
    Location:1283 → 1337
    CCP; Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system
    PHA02927
    Location:1634 → 1873
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:54 → 161
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:1699 → 1752
    Sushi; Sushi repeat (SCR repeat)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    113347915..114561864 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054359698.1 → XP_054215673.1  CUB and sushi domain-containing protein 3 isoform X5

  2. XM_054359697.1 → XP_054215672.1  CUB and sushi domain-containing protein 3 isoform X4

  3. XM_054359696.1 → XP_054215671.1  CUB and sushi domain-containing protein 3 isoform X3

  4. XM_054359694.1 → XP_054215669.1  CUB and sushi domain-containing protein 3 isoform X1

  5. XM_054359695.1 → XP_054215670.1  CUB and sushi domain-containing protein 3 isoform X2

  6. XM_054359699.1 → XP_054215674.1  CUB and sushi domain-containing protein 3 isoform X7

  7. XM_054359700.1 → XP_054215675.1  CUB and sushi domain-containing protein 3 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z407.3 GenPept UniProtKB/Swiss-Prot:Q7Z407

Gene LinkOut

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