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CLCA3P chloride channel accessory 3, pseudogene [ Homo sapiens (human) ]

Gene ID: 9629, updated on 3-Mar-2026
Official Symbol
CLCA3Pprovided by HGNC
Official Full Name
chloride channel accessory 3, pseudogeneprovided by HGNC
Primary source
HGNC:HGNC:2017
See related
Ensembl:ENSG00000291014 MIM:604337; AllianceGenome:HGNC:2017
Gene type
pseudo
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLCA3
Summary
This gene is a transcribed pseudogene belonging to the calcium sensitive chloride conductance protein family. To date, all members of this gene family map to the same site on chromosome 1p31-p22 and share high degrees of homology in size, sequence and predicted structure, but differ significantly in their tissue distributions. This gene contains several nonsense codons compared to other family members that render the transcript a candidate for nonsense-mediated mRNA decay (NMD). Therefore, this gene is unlikely to be protein-coding. [provided by RefSeq, Jan 2009]
Expression
Low expression observed in reference dataset See more
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See CLCA3P in Genome Data Viewer
Location:
1p22.3
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (86634276..86655376)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (86474301..86495405)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (87099959..87121059)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904210 Neighboring gene uncharacterized LOC105378826 Neighboring gene cell division cycle associated 4 pseudogene 2 Neighboring gene chloride channel accessory 4 Neighboring gene CLCA4 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:87075539-87075711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1278 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:87113290-87114489 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:87149909-87150556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1279 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:87170097-87170598 Neighboring gene SH3 domain containing GRB2 like, endophilin B1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:87221223-87221723 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:87239295-87240494 Neighboring gene ribosomal protein L17 pseudogene 5

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Molecular cloning and biochemical characterization of a truncated, secreted member of the human family of Ca2+-activated Cl- channels. Gruber AD, et al. Biochim Biophys Acta, 1999 Mar 19. PMID 10095065
  2. Clustering of the human CLCA gene family on the short arm of chromosome 1 (1p22-31). Gruber AD, et al. Genome, 1999 Oct. PMID 10584316
  3. Molecular characteristics and functional diversity of CLCA family members. Pauli BU, et al. Clin Exp Pharmacol Physiol, 2000 Nov. PMID 11071307
  4. A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. Xie L, et al. PLoS Genet, 2012. PMID 23284306, Free PMC Article
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

GeneRIFs: Gene References Into Functions

Review eQTL and phenotype association data in this region using PheGenI

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Other Names

  • chloride channel regulator 3 pseudogene
  • chloride channel, calcium activated, family member 3

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.

RNA

  1. NR_024604.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AF043976, AL356270
    Related
    ENST00000466454.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_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
    86634276..86655376
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    86474301..86495405
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004921.2: Suppressed sequence

    Description
    NM_004921.2: This RefSeq was permanently suppressed because it is now thought that this gene does not encode a protein.
Nucleotide Protein
Heading Accession and Version

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