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    CSMD2 CUB and Sushi multiple domains 2 [ Homo sapiens (human) ]

    Gene ID: 114784, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CSMD2provided by HGNC
    Official Full Name
    CUB and Sushi multiple domains 2provided by HGNC
    Primary source
    HGNC:HGNC:19290
    See related
    Ensembl:ENSG00000121904 MIM:608398; AllianceGenome:HGNC:19290
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    dJ947L8.1; dJ1007G16.1; dJ1007G16.2
    Summary
    The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See CSMD2 in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    74
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33513998..34165842, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33375608..34027570, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33979598..34631443, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33975098-33976006 Neighboring gene proteasome 20S subunit alpha 3 pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33985189-33985725 Neighboring gene zinc finger and SCAN domain containing 20 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_7293 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:34070585-34071784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34073563-34074063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34073062-34073562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34099135-34099641 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:34100609-34101540 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:34101541-34102471 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:34102434-34102604 Neighboring gene uncharacterized LOC124903976 Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 14 Neighboring gene CSMD2 antisense RNA 1 Neighboring gene high mobility group box 4 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:34484896-34485714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34503797-34504791 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:34516720-34516822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34526371-34526872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:34526873-34527372 Neighboring gene NANOG hESC enhancer GRCh37_chr1:34553505-34554025 Neighboring gene RNA, 5S ribosomal pseudogene 42 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 711 Neighboring gene Sharpr-MPRA regulatory region 230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:34644818-34645318 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:34653982-34654535 Neighboring gene chromosome 1 open reading frame 94 Neighboring gene ferritin, heavy polypeptide 1 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. A genetic association study of CSMD1 and CSMD2 with cognitive function. Athanasiu L, et al. Brain Behav Immun, 2017 Mar. PMID 27890662
    2. Loss of CSMD1 or 2 may contribute to the poor prognosis of colorectal cancer patients. Zhang R, et al. Tumour Biol, 2014 May. PMID 24408017
    3. The complement control-related genes CSMD1 and CSMD2 associate to schizophrenia. Håvik B, et al. Biol Psychiatry, 2011 Jul 1. PMID 21439553
    4. Identification of two new members of the CSMD gene family. Lau WL, et al. Genomics, 2003 Sep. PMID 12906867
    5. Genome-wide association study identifies GPC5 as a novel genetic locus protective against sudden cardiac arrest. Arking DE, et al. PLoS One, 2010 Mar 25. PMID 20360844, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CSMD1 and CSMD2 expressions were associated with overall survival
      Title: Loss of CSMD1 or 2 may contribute to the poor prognosis of colorectal cancer patients.
    2. data demonstrate a significant role of complement control-related genes in the etiology of schizophrenia.
      Title: The complement control-related genes CSMD1 and CSMD2 associate to schizophrenia.
    3. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    4. 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.
    5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study identifies GPC5 as a novel genetic locus protective against sudden cardiac arrest.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    7. CSMD2 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
    Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
    EBI GWAS Catalog
    Genome-wide association study of intelligence: additive effects of novel brain expressed genes.
    EBI GWAS Catalog
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    EBI GWAS Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    EBI GWAS Catalog
    Voxelwise genome-wide association study (vGWAS).
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1884

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in maintenance of postsynaptic density structure IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in postsynaptic density assembly IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    CUB and sushi domain-containing protein 2
    Names
    CUB and Sushi (SCR repeat) domain
    CUB and sushi multiple domains protein 2

    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.

    Genomic

    1. NG_053181.1 RefSeqGene

      Range
      5613..656845
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001281956.2 → NP_001268885.1  CUB and sushi domain-containing protein 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB212622, AC115285, AK095627, AY210418
      Consensus CDS
      CCDS60082.1
      UniProtKB/TrEMBL
      A0A087X0K4
      Related
      ENSP00000362479.4, ENST00000373381.9
      Conserved Domains (6) summary
      cd00033
      Location:561 → 615
      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:179 → 236
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
      cd00041
      Location:618 → 725
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00431
      Location:1485 → 1590
      CUB; CUB domain
      pfam00084
      Location:2292 → 2349
      Sushi; Sushi repeat (SCR repeat)
      cl27761
      Location:2792 → 3032
      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_052896.5 → NP_443128.2  CUB and sushi domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_443128.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and contains multiple differences in the coding region, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AB212622, AC115285, AC115286, AK095627, AY210418
      Consensus CDS
      CCDS380.1
      UniProtKB/Swiss-Prot
      B1AM50, E7EUA6, Q53TY4, Q5VT59, Q7Z408, Q8N963, Q96Q03, Q9H4V7, Q9H4V8, Q9H4V9, Q9H4W0, Q9H4W1, Q9H4W2, Q9H4W3, Q9H4W4, Q9HCY5, Q9HCY6, Q9HCY7
      UniProtKB/TrEMBL
      A0A087X0K4
      Related
      ENSP00000362486.3, ENST00000373388.7
      Conserved Domains (6) summary
      cd00033
      Location:2658 → 2711
      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:139 → 196
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
      PHA02927
      Location:2947 → 3186
      PHA02927; secreted complement-binding protein; Provisional
      cd00041
      Location:578 → 685
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00084
      Location:2294 → 2351
      Sushi; Sushi repeat (SCR repeat)
      pfam00431
      Location:1445 → 1550
      CUB; CUB domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      33513998..34165842 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443685.1 → XP_047299641.1  CUB and sushi domain-containing protein 2 isoform X9

      Related
      ENSP00000483463.1, ENST00000619121.4

    2. XM_047443656.1 → XP_047299612.1  CUB and sushi domain-containing protein 2 isoform X3

    3. XM_047443666.1 → XP_047299622.1  CUB and sushi domain-containing protein 2 isoform X5

    4. XM_047443642.1 → XP_047299598.1  CUB and sushi domain-containing protein 2 isoform X2

    5. XM_047443607.1 → XP_047299563.1  CUB and sushi domain-containing protein 2 isoform X1

    6. XM_017000185.2 → XP_016855674.1  CUB and sushi domain-containing protein 2 isoform X1

      UniProtKB/TrEMBL
      A0A087X0K4
      Conserved Domains (6) summary
      cd00033
      Location:2656 → 2709
      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:179 → 236
      CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
      PHA02927
      Location:2767 → 3007
      PHA02927; secreted complement-binding protein; Provisional
      cd00041
      Location:618 → 725
      CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
      pfam00084
      Location:2292 → 2349
      Sushi; Sushi repeat (SCR repeat)
      pfam00431
      Location:1485 → 1590
      CUB; CUB domain

    7. XM_047443661.1 → XP_047299617.1  CUB and sushi domain-containing protein 2 isoform X4

    8. XM_017000191.2 → XP_016855680.1  CUB and sushi domain-containing protein 2 isoform X6

    9. XM_017000193.2 → XP_016855682.1  CUB and sushi domain-containing protein 2 isoform X8

    10. XM_017000192.2 → XP_016855681.1  CUB and sushi domain-containing protein 2 isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      33375608..34027570 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334092.1 → XP_054190067.1  CUB and sushi domain-containing protein 2 isoform X1

    2. XM_054334093.1 → XP_054190068.1  CUB and sushi domain-containing protein 2 isoform X6

    3. XM_054334094.1 → XP_054190069.1  CUB and sushi domain-containing protein 2 isoform X8

    RNA

    1. XR_008485892.1 RNA Sequence

    2. XR_008485889.1 RNA Sequence

    3. XR_008485887.1 RNA Sequence

    4. XR_008485888.1 RNA Sequence

    5. XR_008485891.1 RNA Sequence

    6. XR_008485890.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z408.2 GenPept UniProtKB/Swiss-Prot:Q7Z408

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