Alternative titles; symbols
HGNC Approved Gene Symbol: CLCN7
SNOMEDCT: 725050005;
Cytogenetic location: 16p13.3 Genomic coordinates (GRCh38) : 16:1,444,935-1,475,028 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 16p13.3 | Hypopigmentation, organomegaly, and delayed myelination and development | 618541 | Autosomal dominant | 3 |
| Osteopetrosis, autosomal dominant 2 | 166600 | Autosomal dominant | 3 | |
| Osteopetrosis, autosomal recessive 4 | 611490 | Autosomal recessive | 3 |
Brandt and Jentsch (1995) identified regions of chloride channel proteins that are highly conserved within a given branch of the CLCN family but show significant divergence between branches. By RT-PCR using degenerate oligonucleotides based on the CLCN6 (602726) sequence within these branch-specific regions, Brandt and Jentsch (1995) cloned a rat brain cDNA encoding Clcn7. Using the rat Clcn7 cDNA to screen a human cerebral cortex cDNA library, they isolated a partial human CLCN7 cDNA which lacked about 15 codons at the 5-prime end. The predicted amino acid sequence of human CLCN7 is 45% identical to that of CLCN6 but only about 21 to 30% identical to the sequences of other known CLCNs. Therefore, Brandt and Jentsch (1995) stated that CLCN6 and CLCN7 together define a new branch of the CLCN family. The human and rat CLCN7 protein sequences are 96% identical. Northern blot analysis revealed that CLCN7 is expressed broadly as an approximately 4.2-kb transcript.
By fluorescence in situ hybridization, Brandt and Jentsch (1995) mapped the CLCN7 gene to 16p13.
Lange et al. (2006) showed that CLCN7 and OSTM1 (607649) proteins colocalize in late endosomes and lysosomes of various tissues, as well as in the ruffled border of bone-resorbing osteoclasts. Coimmunoprecipitations showed that CLCN7 and OSTM1 form a molecular complex and suggested that OSTM1 is a beta subunit of CLCN7. CLCN7 is required for OSTM1 to reach lysosomes, where the highly glycosylated OSTM1 luminal domain is cleaved. Protein but not RNA levels of Clcn7 are greatly reduced in grey-lethal mice, which lack Ostm1, suggesting that the Clcn7-Ostm1 interaction is important for protein stability. As Clcn7 protein levels in Ostm1-deficient tissues and cells, including osteoclasts, are decreased below 10% of normal levels, Ostm1 mutations probably cause osteopetrosis by impairing the acidification of the osteoclast resorption lacuna, which depends on Clcn7. Lange et al. (2006) concluded that their finding that grey-lethal mice, just like Clcn7-deficient mice, show lysosomal storage and neurodegeneration in addition to osteopetrosis implies a more general importance for Clcn7-Ostm1 complexes.
Graves et al. (2008) directly demonstrated an anion transport pathway in lysosomes that has the defining characteristics of a CLC Cl(-)/H(+) antiporter and showed that this transporter is the predominant route for Cl(-) through the lysosomal membrane. Knockdown of Clc7 expression by short interfering RNA could essentially ablate this lysosomal Cl(-)/H(+) antiporter activity and could strongly diminish the ability of lysosomes to acidify in vivo. Graves et al. (2008) concluded that CLC7 is a Cl(-)/H(+) antiporter, that it constitutes the major Cl(-) permeability of lysosomes, and that it is important in lysosomal acidification.
Osteopetrosis, Autosomal Recessive 4
Based on the similarity between the phenotype of patients with infantile malignant osteopetrosis (see OPTB4; 611490) and that of mice with targeted disruption of the Clcn7 gene (see ANIMAL MODEL), which develop severe osteopetrosis and retinal degeneration, Kornak et al. (2001) searched for mutations in the human CLCN7 gene in 12 patients with infantile osteopetrosis. They identified compound heterozygosity for a nonsense (Q555X; 602727.0001) and a missense (R762Q; 602727.0002) mutation in the CLCN7 gene in 1 patient with the disease who had early visual impairment. No retinal histology was available.
Blair et al. (2004) grew CD14 cells from normal and 4 osteopetrotic human subjects in the presence of bone and studied their osteoclastic differentiation in vitro. The osteopetrotic cells showed defects in acid transport, organic matrix removal, and cell fusion with deficient attachment compared with the normal cells. Genotype analysis showed that cells from 2 patients compound heterozygous for TCIRG1 (604592) mutations had acid transport defects, whereas cells from 1 patient compound heterozygous for CLCN7 mutations had organic matrix removal defects. The cells with an attachment defect were from a patient who lacked TCIRG1 and CLCN7 mutations.
Osteopetrosis, Autosomal Dominant 2
In affected individuals from 12 unrelated families with autosomal dominant osteopetrosis-2 (OPTA2; 166600), Cleiren et al. (2001) identified heterozygosity for 7 different mutations in the CLCN7 gene (see, e.g., 602727.0004 and 602727.0005). Analysis of microsatellite markers indicated that the mutations arose independently in each family. Among these families was the Danish family that Van Hul et al. (1997) initially linked to chromosome 1p21. Additionally, Cleiren et al. (2001) identified 1 patient with the severe autosomal recessive infantile form of osteopetrosis (OPTB4) who was homozygous for a CLCN7 missense mutation (L766P; 602727.0003), for which her asymptomatic parents were heterozygous. The authors hypothesized that OPTA2 reflects a dominant-negative effect, since loss-of-function mutations in CLCN7 do not cause abnormalities in heterozygous individuals.
Hypopigmentation, Organomegaly, and Delayed Myelination and Development
In 2 unrelated children with hypopigmentation, organomegaly, and delayed myelination and development (HOD; 618541), Nicoli et al. (2019) identified heterozygosity for the same de novo missense mutation in the CLCN7 gene (Y715C; 602727.0007). Neither child exhibited osteopetrosis. Functional analysis demonstrated that the mutation caused a gain of function.
Kornak et al. (2001) observed that mice with targeted disruption of the Clcn7 gene (Clcn7 -/-) had severe osteopetrosis and retinal degeneration. Although osteoclasts were present in normal numbers, they failed to resorb bone because they could not acidify the extracellular resorption lacuna. Clcn7 was found to reside in late endosomal and lysosomal compartments. In osteoclasts it was highly expressed in the ruffled membrane, formed by the fusion of H(+) ATPase-containing vesicles, that secretes protons into the lacuna. The authors concluded that CLCN7 provides the chloride conductance required for an efficient proton pumping by the H(+) ATPase of the osteoclast ruffled membrane.
Kasper et al. (2005) showed that Clcn7 knockout mice, in addition to osteopetrosis, display neurodegeneration and severe lysosomal storage disease despite unchanged lysosomal pH in cultured neurons. Rescuing their bone phenotype by transgenic expression of Clcn7 in osteoclasts moderately increased the life span and revealed a further progression of the central nervous system pathology. Histologic analysis demonstrated an accumulation of electron-dense material in neurons, autofluorescent structures, microglial activation, and astrogliosis. As in human neuronal ceroid lipofuscinosis (see 256730), there was a strong accumulation of subunit c of the mitochondrial ATP synthase (see 603192) and increased amounts of lysosomal enzymes. Such alterations were minor or absent in Clcn3 (600580) knockout mice, despite a massive neurodegeneration. Osteopetrotic oc/oc mice, lacking a functional proton-ATPase a3 subunit (604592), showed no comparable retinal or neuronal degeneration.
Weinert et al. (2010) generated mice carrying a point mutation converting Clc7 into an uncoupled chloride conductor. Despite maintaining lysosomal conductions and normal lysosomal pH, these Clcn7(unc/unc) mice showed lysosomal storage disease like mice lacking Clc7. However, their osteopetrosis was milder, and they lacked a coat color phenotype. Weinert et al. (2010) concluded that only some roles of ClC7 Cl-/H+ exchange can be taken over by a chloride conductance. This conductance was even deleterious in Clcn7/unc heterozygote mice. Clcn7-null and Clcn7(unc/unc) mice accumulated less chloride in lysosomes than did wildtype mice. Weinert et al. (2010) concluded that lowered lysosomal chloride may underlie their common phenotypes.
Nicoli et al. (2019) generated mice with a knock-in of Clcn7 Y713C, the variant orthologous to the human CLCN7 Y715C variant (602727.0007), and observed recapitulation of the human phenotype, including striking hair hypopigmentation; dermal fibroblasts with enlarged cytoplasmic vacuoles; lysosomal storage with intracellular vacuoles in the liver, spleen, and kidneys; brain myelination abnormalities; and enlarged cytoplasmic vacuoles in dermal fibroblasts that partially stained for Lamp1 (153330). Tibial sections from mutant mice revealed no osteopetrosis and showed an intact marrow cavity and normally organized trabecular and cortical structure.
Pressey et al. (2010) studied the neurologic phenotype of a Clcn7 knockout mouse model. The mutant mice had atrophy image of the cortex, corpus callosum, internal capsule, and cerebral peduncles at 4 weeks of age. The mouse brains also had early-onset and progressive astrocytosis of the thalamus and cortex. Microglial activation was identified in the same regions as the astrocytosis. There was also storage of carbohydrate material in neuronal lysosomes throughout the cortex and thalamus.
In a patient with autosomal recessive infantile malignant osteopetrosis (OPTB4; 611490), Kornak et al. (2001) identified compound heterozygosity for 2 mutations in the CLCN7 gene: a C-to-T transition in exon 18, leading to a gln555-to-ter substitution, and a 2285G-A transition in exon 24, leading to an arg762-to-gln (R762Q; 602727.0002) substitution. The R762Q substitution abolished a positive charge within the conserved CBS2 domain of CCLN7. To investigate whether the mutations affected protein expression, fibroblasts were analyzed by Western blot analysis and immunofluorescence. In contrast to control cells, CLCN7 protein could not be detected in the fibroblasts from the patient.
For discussion of the arg762-to-gln (R762Q) mutation that was identified in a patient with autosomal recessive osteopetrosis-4 (OPTB4; 611490) by Kornak et al. (2001), see 602727.0001.
In a girl with autosomal recessive infantile malignant osteopetrosis (OPTB4; 611490), born to second-cousin parents of Chinese ancestry, Cleiren et al. (2001) identified homozygosity for a T-to-C transition at codon 766 of the CLCN7 gene, leading to a leu766-to-pro (L766P) substitution. The substitution was located in the D13 stretch of the conserved CBS2 domain. The asymptomatic parents were heterozygous for the mutation, which was not found in 100 control chromosomes.
In a French family and an American family with autosomal dominant osteopetrosis (OPTA2; 166600), previously studied by Benichou et al. (2001) and Yoneyama et al. (1992), respectively, Cleiren et al. (2001) identified heterozygosity for a C-to-T transition at codon 767 of the CLCN7 gene, leading to an arg767-to-trp (R767W) substitution. The substitution abolished a positive charge within the conserved CBS2 domain of CLCN7. Analysis of microsatellite markers indicated that the mutation arose independently in each family.
In a French family and an American family with autosomal dominant osteopetrosis (OPTA2; 166600), Cleiren et al. (2001) identified heterozygosity for a dinucleotide deletion (2423delAG) in the C-terminal portion of CLCN7. The mutation was predicted to generate a frameshift and result in substitutions for the last 10 amino acids of the protein. The French family had previously been reported by Benichou et al. (2001). Analysis of microsatellite markers indicated that the mutation arose independently in each family.
In a Chinese sister and brother with malignant osteopetrosis (OPTB4; 611490), born of first-cousin parents, Lam et al. (2007) identified homozygosity for a c.781A-T transversion in exon 9 of the CLCN7 gene, resulting in an ile261-to-phe (I261F) substitution. Their unaffected parents and an unaffected brother were heterozygous for the mutation, which was not found in 50 Chinese controls.
In a 22-month-old Caucasian girl and a 14-month-old Ghanaian boy with hypopigmentation, organomegaly, and delayed myelination and development (HOD; 618541), Nicoli et al. (2019) identified heterozygosity for a de novo c.2144A-G transition (c.2144A-G, NM_001287.5) in exon 23 of the CLCN7 gene, resulting in a tyr715-to-cys (Y715C) substitution at a highly conserved residue within the C-terminal cytoplasmic domain. The mutation was not found in the unaffected parents or in the ExAC, gnomAD, ESP, or EVS databases. Functional analysis of chloride transport in transfected Xenopus oocytes demonstrated an approximately 3-fold increase in outward currents with the Y715C mutant compared to wildtype. Quantitative pH measurements in lysosomes from patient fibroblasts revealed a reduced pH compared to control; increased staining with acidotropic dye confirmed the lowered lysosomal pH. Large, variably sized cytoplasmic single- and double-membraned vacuoles, sometimes containing amorphous material and cellular debris, were present in fibroblasts from both probands, and overexpressing the Y715C variant in control fibroblasts dramatically recapitulated the mutant phenotype of enlarged cytoplasmic vacuoles. Chloroquine treatment of patient dermal fibroblasts increased lysosomal pH in a dose-dependent manner and reduced the abundance of large vacuoles in the mutant cells.
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