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

Gene ID: 114784, updated on 1-Mar-2024

Summary

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
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Genomic context

See CSMD2 in Genome Data Viewer
Location:
1p35.1
Exon count:
74
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (33513998..34165842, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (33375608..34027570, complement)
105.20220307 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • KIAA1884

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

NEW Try the new Transcript table

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_001281956.2NP_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:561615
    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:179236
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    cd00041
    Location:618725
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00431
    Location:14851590
    CUB; CUB domain
    pfam00084
    Location:22922349
    Sushi; Sushi repeat (SCR repeat)
    cl27761
    Location:27923032
    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_052896.5NP_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:26582711
    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:139196
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:29473186
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:578685
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:22942351
    Sushi; Sushi repeat (SCR repeat)
    pfam00431
    Location:14451550
    CUB; CUB domain

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_000001.11 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A087X0K4
    Related
    ENSP00000483463.1, ENST00000619121.4
  2. XM_047443656.1XP_047299612.1  CUB and sushi domain-containing protein 2 isoform X3

    UniProtKB/TrEMBL
    A0A087X0K4
  3. XM_047443666.1XP_047299622.1  CUB and sushi domain-containing protein 2 isoform X5

    UniProtKB/TrEMBL
    A0A087X0K4
  4. XM_047443642.1XP_047299598.1  CUB and sushi domain-containing protein 2 isoform X2

    UniProtKB/TrEMBL
    A0A087X0K4
  5. XM_047443607.1XP_047299563.1  CUB and sushi domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A087X0K4
  6. XM_017000185.2XP_016855674.1  CUB and sushi domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A087X0K4
    Conserved Domains (6) summary
    cd00033
    Location:26562709
    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:179236
    CCP; Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR)
    PHA02927
    Location:27673007
    PHA02927; secreted complement-binding protein; Provisional
    cd00041
    Location:618725
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    pfam00084
    Location:22922349
    Sushi; Sushi repeat (SCR repeat)
    pfam00431
    Location:14851590
    CUB; CUB domain
  7. XM_047443661.1XP_047299617.1  CUB and sushi domain-containing protein 2 isoform X4

    UniProtKB/TrEMBL
    A0A087X0K4
  8. XM_017000191.2XP_016855680.1  CUB and sushi domain-containing protein 2 isoform X6

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

  10. XM_017000192.2XP_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_054334092.1XP_054190067.1  CUB and sushi domain-containing protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A087X0K4
  2. XM_054334093.1XP_054190068.1  CUB and sushi domain-containing protein 2 isoform X6

  3. XM_054334094.1XP_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