Alternative titles; symbols
HGNC Approved Gene Symbol: CLIC2
Cytogenetic location: Xq28 Genomic coordinates (GRCh38): X:155,276,211-155,334,614 (from NCBI)
The CLIC2 gene encodes a protein that belongs to a class of soluble and membrane-bound proteins named because the first members of this family formed intracellular chloride channels. The CLIC2 protein is structurally similar to CLIC1 (602872) and to a form of glutathione transferase (GSTO1; 605482), but has no transferase activity. CLIC2 functions as a regulator of calcium homeostasis in cardiac myocytes via interaction with the cardiac ryanodine receptor (RYR2; 180902) (summary by Board et al., 2004).
As part of an effort to produce a transcript map of the Xq28 chromosomal region, Rogner et al. (1996) characterized a cDNA that they designated XAP121, or CLIC2. Heiss and Poustka (1997) reported that the predicted 243-amino acid CLIC2 protein shares 60% identity with the CLIC1 protein, a nuclear chloride channel. Using RT-PCR, Rogner et al. (1996) found that CLIC2 is expressed in fetal liver and adult skeletal muscle. No signal was detected on Northern blots.
Board et al. (2004) stated that the predicted CLIC2 protein has a molecular mass of 27.8 kD. The protein sequence showed 58.8% identity to CLIC1 and 18.6% identity to GSTO1. Northern blot analysis detected 2 abundant mRNA species of 1.45 and 2.37 kb, and a third less abundant species of 0.8 kb. The 2 larger mRNA transcripts were widely distributed in human tissues, with highest expression in lung and spleen and lesser expression in heart, liver, and skeletal muscle.
Using RT-PCR, Takano et al. (2012) found expression of the CLIC2 gene in all fetal tissues, including brain.
Heiss and Poustka (1997) found that the CLIC2 gene contains 6 exons.
Rogner et al. (1996) identified the CLIC2 gene on chromosome Xq28.
Board et al. (2004) demonstrated that CLIC2 is a strong inhibitor of the cardiac ryanodine receptor (RYR2) calcium release channels in both lipid bilayers and in cardiac sarcoplasmic reticulum vesicles, suggesting that it contributes to intracellular calcium homeostasis by regulating its release from internal stores in the cell.
Dulhunty et al. (2005) demonstrated that CLIC2 reduces activation of the RYR2 channel by its primary endogenous ligands ATP and calcium. When CLIC2 was added to the cytoplasmic side of RYR2 channels in lipid bilayers, RYR2 activity was depressed in a reversible, voltage-independent manner. The authors concluded that CLIC2 may act physiologically as a cytosolic inhibitor of RYR2 channels during diastole and during stress.
Reclassified Variants
The H101Q variant in the CLIC2 gene (300138.0001) that was identified in 2 brothers (family K8015) with syndromic X-linked intellectual developmental disorder (see 300886) by Takano et al. (2012) has been reclassified as a variant of unknown significance.
This variant, formerly titled INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC 32 based on the report of Takano et al. (2012), has been reclassified based on a review of the gnomAD database by Hamosh (2024).
In 2 brothers (family K8015) with X-linked syndromic intellectual developmental disorder-32 (MRXS32; 300886), Takano et al. (2012) identified a hemizygous c.303C-G transversion in the CLIC2 gene, resulting in a his101-to-gln (H101Q) substitution at a highly conserved residue in the joint region. The mutation was not found in 1,059 normal individuals, but was inherited from the mother who had mild learning disabilities. The mutation was identified by exome capture and deep sequencing. COS-7 and PC-12 cells expressing the mutation showed normal cell morphology and neurite length, and there was normal localization of the mutant protein, which appeared to fold normally. However, the mutant protein had increased thermal stability compared to wildtype. In lipid bilayers, the mutant H101Q protein resulted in an increase in both the skeletal RYR1 (180901) and cardiac RYR2 (180902) channels being in the open probability states, which was a reversal of the effect of wildtype CLIC2. Three-dimensional predictions indicated that the H101Q mutation affected the binding affinity to RYR channels, resulting in stronger and more stable binding compared to wildtype. The authors noted that folding free energy calculations by Witham et al. (2011) had predicted that the H101Q mutant is more stable than wildtype. Overall, the data suggested that mutant CLIC2 would stimulate the release of calcium by keeping the RYR channels in the open state, resulting in overly active RYR2 in heart muscle with excess potential firing in those cells. There was also some evidence that the mutation may impair insertion of CLIC2 into the membrane to form a functioning ion channel.
Hamosh (2024) noted that the c.303C-G variant was present in too many males in the gnomAD database (v4.1) to account for this phenotype.
Board, P. G., Coggan, M., Watson, S., Gage, P. W., Dulhunty, A. F. CLIC-2 modulates cardiac ryanodine receptor Ca(2+) release channels. Int. J. Biochem. Cell Biol. 36: 1599-1612, 2004. [PubMed: 15147738] [Full Text: https://doi.org/10.1016/j.biocel.2004.01.026]
Dulhunty, A. F., Pouliquin, P., Coggan, M., Gage, P. W., Board, P. G. A recently identified member of the glutathione transferase structural family modifies cardiac RyR2 substate activity, coupled gating and activation by Ca(2+) and ATP. Biochem. J. 390: 333-343, 2005. [PubMed: 15916532] [Full Text: https://doi.org/10.1042/BJ20042113]
Hamosh, A. Personal Communication. Baltimore, Md. 5/20/2024.
Heiss, N. S., Poustka, A. Genomic structure of a novel chloride channel gene, CLIC2, in Xq28. Genomics 45: 224-228, 1997. [PubMed: 9339381] [Full Text: https://doi.org/10.1006/geno.1997.4922]
Rogner, U. C., Heiss, N. S., Kioschis, P., Wiemann, S., Korn, B., Poustka, A. Transcriptional analysis of the candidate region for incontinentia pigmenti (IP2) in Xq28. Genome Res. 6: 922-934, 1996. [PubMed: 8908511] [Full Text: https://doi.org/10.1101/gr.6.10.922]
Takano, K., Liu, D., Tarpey, P., Gallant, E., Lam, A., Witham, S., Alexov, E., Chaubey, A., Stevenson, R. E., Schwartz, C. E., Board, P. G., Dulhunty, A. F. An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity. Hum. Molec. Genet. 21: 4497-4507, 2012. [PubMed: 22814392] [Full Text: https://doi.org/10.1093/hmg/dds292]
Witham, S., Takano, K., Schwartz, C., Alexov, E. A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics. Proteins 79: 2444-2454, 2011. [PubMed: 21630357] [Full Text: https://doi.org/10.1002/prot.23065]