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

Gene ID: 114784, updated on 2-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 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)

Genotypes

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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