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COLCA1 colorectal cancer associated 1 [ Homo sapiens (human) ]

Gene ID: 399948, updated on 5-Mar-2024

Summary

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Official Symbol
COLCA1provided by HGNC
Official Full Name
colorectal cancer associated 1provided by HGNC
Primary source
HGNC:HGNC:33789
See related
Ensembl:ENSG00000196167 MIM:615693; AllianceGenome:HGNC:33789
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CASC12; C11orf92; LOH11CR1F
Summary
This gene encodes a transmembrane protein that localizes to granular structures, including crystalloid eosinophilic granules and other granular organelles. This gene, along with an overlapping opposite strand gene, has been implicated as a susceptibility locus for colorectal cancer. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression
Broad expression in stomach (RPKM 15.6), prostate (RPKM 11.1) and 14 other tissues See more
Orthologs
all
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Genomic context

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See COLCA1 in Genome Data Viewer
Location:
11q23.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (111293389..111305048, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (111303576..111315229, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (111164114..111175773, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723966 Neighboring gene ribosomal protein S17 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5504 Neighboring gene POU class 2 homeobox associating factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3894 Neighboring gene POU class 2 homeobox associating factor 3 Neighboring gene uncharacterized LOC105369491 Neighboring gene uncharacterized LOC124902755

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. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. Closa A, et al. Carcinogenesis, 2014 Sep. PMID 24760461, Free PMC Article
  2. Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1. Biancolella M, et al. Hum Mol Genet, 2014 Apr 15. PMID 24256810, Free PMC Article
  3. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. Hitomi Y, et al. Sci Rep, 2021 Feb 25. PMID 33633225, Free PMC Article
  4. Enrichment of low penetrance susceptibility loci in a Dutch familial colorectal cancer cohort. Middeldorp A, et al. Cancer Epidemiol Biomarkers Prev, 2009 Nov. PMID 19843678
  5. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Peltekova VD, et al. Int J Cancer, 2014 May 15. PMID 24154973, Free PMC Article

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis.
    Title: rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis.
  2. We found PLCE1, C11orf92-C11orf93, and NOC3L associated with colorectal cancer susceptibility
    Title: Genetic association of PLCE1, C11orf92-C11orf93, and NOC3L with colorectal cancer risk in the Han population.
  3. Data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer.
    Title: Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.
  4. Observational study of gene-disease association, gene-gene interaction, and gene-environment interaction. (HuGE Navigator)
    Title: Low-penetrance susceptibility variants in familial colorectal cancer.
  5. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Susceptibility genetic variants associated with colorectal cancer risk correlate with cancer phenotype.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association studies on 11 published colorectal cancer risk loci.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21.
EBI GWAS Catalog
Identification of Genetic Susceptibility Loci for Colorectal Tumors in a Genome-Wide Meta-analysis.
EBI GWAS Catalog
Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk.
EBI GWAS Catalog
Meta-analysis of new genome-wide association studies of colorectal cancer risk.
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

General gene information

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Markers

Homology

Other Names

  • cancer susceptibility candidate 12
  • colorectal cancer-associated protein 1

Clone Names

  • FLJ45803, DKFZp781P19126

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 

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_027686.2 RefSeqGene

    Range
    5001..16660
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. NR_169237.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000669257.1

  2. NR_169241.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000532918.4

  3. NR_169242.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000355430.4

  4. NR_169243.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448
    Related
    ENST00000540738.3

  5. NR_169244.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448

  6. NR_169245.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AP002448

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    111293389..111305048 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    111303576..111315229 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001302644.1: Suppressed sequence

    Description
    NM_001302644.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

  2. NM_001302645.1: Suppressed sequence

    Description
    NM_001302645.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

  3. NM_001302646.1: Suppressed sequence

    Description
    NM_001302646.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

  4. NM_001302647.1: Suppressed sequence

    Description
    NM_001302647.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

  5. NM_001302648.1: Suppressed sequence

    Description
    NM_001302648.1: This RefSeq was removed because it is now thought that this gene does not encode a protein.

  6. NM_207429.3: Suppressed sequence

    Description
    NM_207429.3: This RefSeq was removed because it is now thought that this gene does not encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZS62.1 GenPept UniProtKB/Swiss-Prot:Q6ZS62

Gene LinkOut

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