CLCN7

gene
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Also known as CLC-7OPTA2CLC7PPP1R63

Summary

CLCN7 (Cl-/H+ antiporter 7, HGNC:2025) is a protein-coding gene on chromosome 16p13.3, encoding H(+)/Cl(-) exchange transporter 7 (P51798). Slowly voltage-gated channel mediating the exchange of chloride ions against protons.

The product of this gene belongs to the CLC chloride channel family of proteins. Chloride channels play important roles in the plasma membrane and in intracellular organelles. This gene encodes chloride channel 7. Defects in this gene are the cause of osteopetrosis autosomal recessive type 4 (OPTB4), also called infantile malignant osteopetrosis type 2 as well as the cause of autosomal dominant osteopetrosis type 2 (OPTA2), also called autosomal dominant Albers-Schonberg disease or marble disease autosoml dominant. Osteopetrosis is a rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. OPTA2 is the most common form of osteopetrosis, occurring in adolescence or adulthood.

Source: NCBI Gene 1186 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): hypopigmentation, organomegaly, and delayed myelination and development (Definitive, ClinGen) — +4 more curated relationships
  • GWAS associations: 2
  • Clinical variants (ClinVar): 1,460 total — 39 pathogenic, 47 likely-pathogenic
  • Phenotypes (HPO): 117
  • MANE Select transcript: NM_001287

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2025
Approved symbolCLCN7
NameCl-/H+ antiporter 7
Location16p13.3
Locus typegene with protein product
StatusApproved
AliasesCLC-7, OPTA2, CLC7, ClC-7, PPP1R63
Ensembl geneENSG00000103249
Ensembl biotypeprotein_coding
OMIM602727
Entrez1186

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 17 protein_coding, 9 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000262318, ENST00000382745, ENST00000561665, ENST00000563642, ENST00000563822, ENST00000564568, ENST00000564968, ENST00000565092, ENST00000566812, ENST00000567139, ENST00000567789, ENST00000567836, ENST00000569851, ENST00000699947, ENST00000699948, ENST00000699950, ENST00000892992, ENST00000892993, ENST00000892994, ENST00000892995, ENST00000892996, ENST00000892997, ENST00000892998, ENST00000917692, ENST00000917693, ENST00000917694, ENST00000971708, ENST00000971709

RefSeq mRNA: 2 — MANE Select: NM_001287 NM_001114331, NM_001287

CCDS: CCDS32361

Canonical transcript exons

ENST00000382745 — 25 exons

ExonStartEnd
ENSE0000087360514748341475028
ENSE0000116431314492761449327
ENSE0000116431614504971450666
ENSE0000116432314516231451716
ENSE0000116433714544111454465
ENSE0000116434014551341455250
ENSE0000116434414557311455795
ENSE0000116437114591071459187
ENSE0000116437714604181460527
ENSE0000116438514608161460948
ENSE0000128204914527551452893
ENSE0000128205514538341453894
ENSE0000258915414449351446717
ENSE0000349199914489661449093
ENSE0000352632914483551448484
ENSE0000355668014652671465338
ENSE0000362691314576941457756
ENSE0000363958314616031461674
ENSE0000364144614470061447086
ENSE0000364319314561131456206
ENSE0000365108814614051461470
ENSE0000365555914473921447568
ENSE0000367454514476551447714
ENSE0000369336414486811448766
ENSE0000378815614572541457337

Expression profiles

Bgee: expression breadth ubiquitous, 296 present calls, max score 97.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.5983 / max 542.4659, expressed in 1816 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
15584921.41241812
1558486.70091680
1558450.343990
1558470.133929
1558460.00723

Top tissues by expression

299 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
metanephros cortexUBERON:001053397.61gold quality
right adrenal gland cortexUBERON:003582797.24gold quality
left adrenal gland cortexUBERON:003582597.08gold quality
right adrenal glandUBERON:000123396.91gold quality
adrenal cortexUBERON:000123596.91gold quality
left adrenal glandUBERON:000123496.90gold quality
right hemisphere of cerebellumUBERON:001489096.85gold quality
stromal cell of endometriumCL:000225596.66gold quality
granulocyteCL:000009496.55gold quality
right lobe of thyroid glandUBERON:000111996.40gold quality
left lobe of thyroid glandUBERON:000112096.06gold quality
cerebellar hemisphereUBERON:000224596.05gold quality
spleenUBERON:000210696.02gold quality
cerebellar cortexUBERON:000212995.96gold quality
adrenal glandUBERON:000236995.76gold quality
adenohypophysisUBERON:000219695.63gold quality
small intestine Peyer’s patchUBERON:000345495.56gold quality
right frontal lobeUBERON:000281095.38gold quality
thyroid glandUBERON:000204695.29gold quality
pituitary glandUBERON:000000795.28gold quality
body of stomachUBERON:000116195.26gold quality
endocervixUBERON:000045895.10gold quality
left testisUBERON:000453395.03gold quality
skin of legUBERON:000151195.01gold quality
cerebellumUBERON:000203794.96gold quality
mucosa of stomachUBERON:000119994.91gold quality
upper lobe of left lungUBERON:000895294.88gold quality
monocyteCL:000057694.86gold quality
right testisUBERON:000453494.85gold quality
mononuclear cellCL:000084294.78gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.04

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MITF

miRNA regulators (miRDB)

42 targeting CLCN7, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4283100.0066.422097
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-449299.8768.253611
HSA-MIR-132199.8465.301811
HSA-MIR-473999.8465.251832
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-6764-5P99.7567.892304
HSA-MIR-317599.6566.302031
HSA-MIR-6797-5P99.6166.552084
HSA-MIR-613299.6065.831554
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-1915-3P99.5866.791988
HSA-MIR-76299.5866.611994
HSA-MIR-4649-3P99.5666.901783
HSA-MIR-7106-5P99.5367.473574
HSA-MIR-1207-5P99.4969.112983
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-128-2-5P99.3360.83311
HSA-MIR-128-1-5P99.3360.46332
HSA-MIR-450599.2767.812678
HSA-MIR-472199.2666.05818
HSA-MIR-578799.2267.862628
HSA-MIR-4763-3P99.1067.832649
HSA-MIR-60898.9367.832013
HSA-MIR-330-5P98.7367.631788
HSA-MIR-423-5P98.6967.481522
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-3184-5P98.5667.131491
HSA-MIR-6776-5P98.5467.431304

Literature-anchored findings (GeneRIF, showing 40)

  • clcn7 gene mutation is associated with intermediate autosomal recessive osteopetrosis (PMID:12522560)
  • mutations in the CICN7 gene are responsible for autosomal dominant osteopetrosis, type II, an uncommon sclerosing bone disorder (PMID:12929941)
  • ClCN7 mutations have roles in severe recessive, dominant, and intermediate osteopetrosis (PMID:14584882)
  • ClC-7 has a role in causing autosomal dominant osteopetrosis type II (PMID:15111300)
  • The study indicates that the V418M polymorphism of CLCN7 contributes to the genetic regulation of femoral neck BMD in women. (PMID:16234969)
  • Significant association of CLCN7 polymorphisms with the variance of bone density in postmenopausal women with osteopetrosis. (PMID:16368748)
  • Autosomal dominant osteopetrosis caused by mutations in the CLCN7 gene is a frequently symptomatic disease manifested by a high rate of fracture, osteomyelitis, visual loss, and occasional bone marrow failure. (PMID:17164308)
  • ClC-7 is a Cl-/H+ antiporter; it constitutes the major Cl- permeability of lysosomes, and it is important in lysosomal acidification. (PMID:18449189)
  • Genetic variation in the CLCN7 gene is not a major contributor to the variability in peak BMD at the femoral neck and lumber spine in healthy premenopausal white women and in white men (PMID:18755304)
  • These data demonstrate that ClC-7 is essential for bone resorption, via its role in acidification of the lysosomes and resorption lacunae in osteoclasts (PMID:19070589)
  • Findings suggest that the novel Glu798FS mutation in exon 25 and R767W in exon 24 in the CLCN7 gene were responsible for autosomal dominant osteopetrosis (type II) in two Chinese patients. (PMID:19288050)
  • Mutations in TCIRG1, OSTM1, ClCN7, and TNFRSF11A genes were detected in nine, three, one, and one patientswith infantile malignant osteopetrosis, respectively. (PMID:19507210)
  • results suggest that osteoclastic ClC7 Cl(-) channels are activated under extracellar acidification and suppressed in Clcn7 mutant associated with autosomal osteopetrosis type II during bone resorption. (PMID:19543743)
  • We report on the fatal clinical course of a 3 year old male Turkish patient suffering from osteopetrosis caused by a homozygous mutation in the chloride channel gene ClCN7 with developing pancytopenia and severe neurological impairment. (PMID:19904698)
  • The characterization of 25 unpublished patients has resulted in the identification of 20 novel mutations, including 11 missense mutations, 6 causing premature termination, 1 small deletion and 2 putative splice site defects and clinical heterogeneity. (PMID:19953639)
  • That the CLCN7 mutations provoke a phenotype as severe as the one caused by TCIRG1 loss of function suggests the affected residues to be crucial for the function of the ClC-7 chloride channel or chloride/proton-exchanger (PMID:20424301)
  • Elevated serum LDH isoenzymes and AST indicate a disturbance (of uncertain clinical significance) within multiple extraosseous tissues when there is CLCN7 deficiency. (PMID:20499337)
  • Rat G213R ClC-7 is the analogue of human G215R ClC-7 responsible for autosomal dominant osteopetrosis type II. (PMID:20830208)
  • The authors show that both the aminoterminus and transmembrane span of the Ostm1 beta-subunit are required for ClC-7 Cl(-)/H(+)-exchange, whereas the Ostm1 transmembrane domain suffices for its ClC-7-dependent trafficking to lysosomes. (PMID:21527911)
  • Eight mutations, including two reported mutations (R767W and E798FS) and six novel mutations (E313K, A316G, R743W, G741R, W127G and S290F), were detected in the CLCN7 gene from 12 living autosomal dominant osteopetrosis type II patients. (PMID:21947783)
  • recurrent p.Gly215Arg mutation and novel missense mutations p.Ala299Val and p.Trp319Arg in the CLCN7 gene were responsible for these three Chinese ADO-II families. (PMID:23953223)
  • ClC-7 does not appear to be crucially involved in gastric acid secretion, which explains the absence of an osteopetrorickets phenotype in CLCN7-related osteopetrosis. (PMID:24103576)
  • analysis demonstrates that CLCN7 and TCIRG1 mutations differentially affect bone matrix mineralization, and that there is a need to modify the current classification of osteopetrosis (PMID:24108692)
  • the unusual clinical presentation observed in our patient with a mild clinical onset evolving towards a more serious clinical picture, is associated to two novel mutations on CLCN7 gene. (PMID:25410126)
  • Results show that ClC-7 is strongly expressed in OUMS-27,a chondrocyte cell line and is responsible for Cl- current. Its downregulation during the hypoosmotic stress accompanying osteoarthritis progression is part of the complex etiology of the disease. (PMID:25943117)
  • present findings suggest that the novel missense mutations V289L and A542V in the CLCN7 gene were responsible for autosomal dominant osteopetrosis (type II) in the two Chinese families. (PMID:26056022)
  • The present study identified seven novel mutations of the CLCN7 gene and reported the first case of intermediate autosomal recessive osteopetrosis. with compound heterozygous mutation in the Chinese population. (PMID:26395888)
  • study demonstrates a wide heterogeneity in the progression of the phenotypes and expanded the mutational spectrum for the CLCN7 gene (PMID:26477479)
  • In this study, whole exome sequencing (WES) was successfully used in six patients with malignant infantile osteopetrosis (MIOP) and identified mutations in four MIOP-related genes (CLCN7, TCIRG1, SNX10, and TNFRSF11A). (PMID:27187610)
  • Exome sequencing and Sanger sequencing were conducted in Han Chinese family members, some of whom had typical osteopetrosis, and a novel missense variant c.2350A>T (p.R784W) in the chloride channel 7 gene (CLCN7) was identified. (PMID:27325559)
  • we identified a CLCN7 mutation in a family with autosomal dominant osteopetrosis, RTA, renal stones, epilepsy, and blindness. (PMID:27540713)
  • The present study revealed three novel mutations, showed the dense but brittle sclerotic bones of an autosomal dominant osteopetrosis type II (OPTA2) patient, characterized OPTA2 symptoms from benign to fatal and reported a rare intermediate case of autosomal recessive 4 in a Chinese population. (PMID:28975865)
  • This study was aimed to identify the underlying genetic cause of the disease in a Pakistani family segregating infantile malignant osteopetrosis in autosomal recessive pattern. Two novel homozygous missense variants were found in the same codon 204 of CLCN7 NM_001287.5:c.[610A>T;612C>G] predicting p.(Ser204Trp) variant in the protein. (PMID:29926385)
  • CLCN7 mutation is associated with osteopetrosis. (PMID:30431110)
  • These findings highlighted the vital role of clcn7 in zebrafish craniofacial bone and tooth development and mineralization, revealing novel insights for the causation of osteopetrosis with CLCN7 mutations. (PMID:30867839)
  • Various mutations (R286W, Y746D, Y99C, G793R, E313K, c.22322A>G, P470L and K217X) in the CLCN7 gene were identified in six patients with familial osteopetrosis and one patient with sporadic osteopetrosis. (PMID:30942407)
  • p.Tyr715Cys is a gain-of-function CLCN7 variant associated with developmental delay, organomegaly, and hypopigmentation from lysosomal hyperacidity, abnormal storage, and enlarged intracellular vacuoles. (PMID:31155284)
  • Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1. (PMID:32749217)
  • Identification and Characterization of a Novel CLCN7 Variant Associated with Osteopetrosis. (PMID:33105733)
  • Pathobiologic Mechanisms of Neurodegeneration in Osteopetrosis Derived From Structural and Functional Analysis of 14 ClC-7 Mutants. (PMID:33125761)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioclcn7ENSDARG00000019556
mus_musculusClcn7ENSMUSG00000036636
rattus_norvegicusClcn7ENSRNOG00000016976
drosophila_melanogasterClC-bFBGN0033755
caenorhabditis_elegansWBGENE00000533

Paralogs (8): CLCN6 (ENSG00000011021), CLCN4 (ENSG00000073464), CLCN3 (ENSG00000109572), CLCN2 (ENSG00000114859), CLCN5 (ENSG00000171365), CLCNKB (ENSG00000184908), CLCNKA (ENSG00000186510), CLCN1 (ENSG00000188037)

Protein

Protein identifiers

H(+)/Cl(-) exchange transporter 7P51798 (reviewed: P51798)

Alternative names: Chloride channel 7 alpha subunit, Chloride channel protein 7

All UniProt accessions (6): A0A8V8TPE0, A0A8V8TQF3, P51798, H0Y2M6, H3BNG8, I3L470

UniProt curated annotations — full annotation on UniProt →

Function. Slowly voltage-gated channel mediating the exchange of chloride ions against protons. Functions as antiporter and contributes to the acidification of the lysosome lumen and may be involved in maintaining lysosomal pH. The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons. The presence of conserved gating glutamate residues is typical for family members that function as antiporters.

Subunit / interactions. Chloride channel 7 are heteromers of alpha (CLCN7) and beta (OSTM1) subunits.

Subcellular location. Lysosome membrane.

Tissue specificity. Brain and kidney.

Disease relevance. Osteopetrosis, autosomal recessive 4 (OPTB4) [MIM:611490] A rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. Recessive osteopetrosis commonly manifests in early infancy with macrocephaly, feeding difficulties, evolving blindness and deafness, bone marrow failure, severe anemia, and hepatosplenomegaly. Deafness and blindness are generally thought to represent effects of pressure on nerves. The disease is caused by variants affecting the gene represented in this entry. Osteopetrosis, autosomal dominant 2 (OPTA2) [MIM:166600] A rare genetic disease characterized by abnormally dense bone, due to defective resorption of immature bone. Osteopetrosis occurs in two forms: a severe autosomal recessive form occurring in utero, infancy, or childhood, and a benign autosomal dominant form occurring in adolescence or adulthood. OPTA2 is the most common form of osteopetrosis, occurring in adolescence or adulthood. It is characterized by sclerosis, predominantly involving the spine, the pelvis and the skull base. The disease is caused by variants affecting the gene represented in this entry. Hypopigmentation, organomegaly, and delayed myelination and development (HOD) [MIM:618541] An autosomal dominant pleiotropic syndrome characterized by skin and hair hypopigmentation, growth and developmental delay, organomegaly including enlarged liver, spleen and kidneys, delayed brain myelination and developmental deficit in motor skills. Skin and liver biopsies show cellular accumulation of large intracellular vacuoles. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the chloride channel (TC 2.A.49) family. ClC-7/CLCN7 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
P51798-11yes
P51798-22

RefSeq proteins (2): NP_001107803, NP_001278* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000644CBS_domDomain
IPR001807ClCFamily
IPR002249CIC-7Family
IPR014743Cl-channel_coreHomologous_superfamily
IPR046342CBS_dom_sfHomologous_superfamily
IPR051280Cl-channel/antiporterFamily

Pfam: PF00571, PF00654

Catalyzed reactions (Rhea), 1 shown:

  • 2 chloride(in) + H(+)(out) = 2 chloride(out) + H(+)(in) (RHEA:29567)

UniProt features (138 total): sequence variant 38, helix 30, strand 23, transmembrane region 10, intramembrane region 7, sequence conflict 7, binding site 5, turn 3, short sequence motif 3, modified residue 3, topological domain 2, domain 2, site 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

9 structures.

PDBMethodResolution (Å)
9G6CELECTRON MICROSCOPY1.8
7CQ5ELECTRON MICROSCOPY2.6
9G6EELECTRON MICROSCOPY2.6
9G6DELECTRON MICROSCOPY2.7
7JM7ELECTRON MICROSCOPY2.82
7CQ6ELECTRON MICROSCOPY3
7CQ7ELECTRON MICROSCOPY3.55
8HVTELECTRON MICROSCOPY3.6
7BXUELECTRON MICROSCOPY3.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P51798-F180.940.44

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 247 (mediates proton transfer from the outer aqueous phase to the interior of the protein; involved in linking h(+) and cl(-) transport); 314 (mediates proton transfer from the protein to the inner aqueous phase)

Ligand- & substrate-binding residues (5): 204; 514; 602; 658–660; 783–786

Post-translational modifications (3): 9, 60, 801

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-2672351Stimuli-sensing channels

MSigDB gene sets: 421 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GOCC_VACUOLAR_MEMBRANE, GOBP_INORGANIC_ANION_TRANSPORT, CHANDRAN_METASTASIS_DN, GOBP_MONOATOMIC_CATION_TRANSPORT, GCM_PRKCG, JAZAG_TGFB1_SIGNALING_DN, GOBP_CHLORIDE_TRANSPORT, GOBP_TRANSEPITHELIAL_TRANSPORT, GOMF_PROTON_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_RESPONSE_TO_PH, DOUGLAS_BMI1_TARGETS_DN, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, GCM_VAV1

GO Biological Process (7): response to pH (GO:0009268), transepithelial chloride transport (GO:0030321), chloride transmembrane transport (GO:1902476), monoatomic ion transport (GO:0006811), chloride transport (GO:0006821), transmembrane transport (GO:0055085), proton transmembrane transport (GO:1902600)

GO Molecular Function (7): chloride channel activity (GO:0005254), ATP binding (GO:0005524), chloride:proton antiporter activity (GO:0062158), nucleotide binding (GO:0000166), protein binding (GO:0005515), chloride transmembrane transporter activity (GO:0015108), antiporter activity (GO:0015297)

GO Cellular Component (4): lysosomal membrane (GO:0005765), membrane (GO:0016020), chloride channel complex (GO:0034707), lysosome (GO:0005764)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Ion channel transport1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
chloride transport2
transport2
chloride transmembrane transporter activity2
response to abiotic stimulus1
transepithelial transport1
monoatomic anion transmembrane transport1
monoatomic anion transport1
inorganic anion transport1
cellular process1
monoatomic cation transmembrane transport1
monoatomic anion channel activity1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
solute:inorganic anion antiporter activity1
proton transmembrane transporter activity1
nucleoside phosphate binding1
heterocyclic compound binding1
binding1
monoatomic anion transmembrane transporter activity1
chloride transmembrane transport1
secondary active transmembrane transporter activity1
lysosome1
lytic vacuole membrane1
cellular anatomical structure1
monoatomic ion channel complex1
lytic vacuole1

Protein interactions and networks

STRING

1613 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLCN7OSTM1Q86WC4999
CLCN7TCIRG1Q13488965
CLCN7PLEKHM1Q9Y4G2908
CLCN7ATP4AP20648834
CLCN7ATP12AP54707826
CLCN7CA2P00918804
CLCN7TNFRSF11AQ9Y6Q6772
CLCN7TNFSF11O14788768
CLCN7SNX10Q9Y5X0719
CLCN7CTSKP43235687
CLCN7LRP5O75197650
CLCN7MCOLN1Q9GZU1597
CLCN7HEPACAMQ14CZ8593
CLCN7ACP5P13686576
CLCN7SYT7O43581566

IntAct

149 interactions, top by confidence:

ABTypeScore
STK25STRNpsi-mi:“MI:0914”(association)0.900
OSTM1CLCN7psi-mi:“MI:0407”(direct interaction)0.790
OSTM1CLCN7psi-mi:“MI:0915”(physical association)0.790
CLCN7OSTM1psi-mi:“MI:0915”(physical association)0.790
CDH1CTNND1psi-mi:“MI:0914”(association)0.730
BIRC7HTRA2psi-mi:“MI:0914”(association)0.640
NDUFA13NDUFS8psi-mi:“MI:0914”(association)0.640
CLCN7LHFPL5psi-mi:“MI:0915”(physical association)0.560
CLCN7SLC38A7psi-mi:“MI:0915”(physical association)0.560
OPRM1CLCN7psi-mi:“MI:0915”(physical association)0.560
CLCN7GDAP1psi-mi:“MI:0915”(physical association)0.560
CD53CLCN7psi-mi:“MI:0915”(physical association)0.560
CLCN7AQP7psi-mi:“MI:0915”(physical association)0.560
CLCN7KCNN3psi-mi:“MI:0915”(physical association)0.560
CLCN7LYVE1psi-mi:“MI:0915”(physical association)0.560
CLCN7SLC66A2psi-mi:“MI:0915”(physical association)0.560
CLCN7TMEM179Bpsi-mi:“MI:0915”(physical association)0.560
GET1CLCN7psi-mi:“MI:0915”(physical association)0.560
CLCN7TLCD4psi-mi:“MI:0915”(physical association)0.560
CLCN7GLE1psi-mi:“MI:0915”(physical association)0.560
CLCN7SPRED1psi-mi:“MI:0915”(physical association)0.560
SLC15A4CLCN7psi-mi:“MI:0915”(physical association)0.560
MANSC1KLRG2psi-mi:“MI:0914”(association)0.530

BioGRID (229): CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Proximity Label-MS), CLCN7 (Proximity Label-MS), CLCN7 (Proximity Label-MS), CLCN7 (Two-hybrid), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS), CLCN7 (Affinity Capture-MS)

ESM2 similar proteins: A6NFX1, A6QQL0, D2HKB0, D3ZG27, F1NCD6, F1NJ67, O09014, O70496, O82390, P51798, P51799, Q17QZ3, Q1JQC1, Q32LQ6, Q3T9M1, Q3T9X0, Q3TIT8, Q4PKH3, Q504N2, Q58CV5, Q5F3N0, Q5R8G5, Q5RB09, Q5T4D3, Q5ZIT9, Q5ZKS8, Q66H95, Q68F72, Q69YG0, Q6AY78, Q6PDE8, Q7SY29, Q8BFQ6, Q8BG19, Q8GX78, Q8IVW8, Q8IZD6, Q8N697, Q8NCC5, Q8NEB5

Diamond homologs: O35454, O70496, P0C197, P51793, P51794, P51795, P51796, P51797, P51798, P51799, P92942, P92943, Q1ZXJ0, Q4PKH3, Q54AX6, Q5RBK4, Q61418, Q75JF3, Q86AZ6, Q8XTT4, Q96282, Q99P66, Q9GKE7, Q9TT16, Q9TTU3, Q9WVD4, O18894, P51790, P51791, P51792, P60300, P92941, Q5RDJ7, Q9R279, O60159, O94287, P35523, P35524, P37020, Q64347

SIGNOR signaling

2 interactions.

AEffectBMechanism
TFEB“up-regulates quantity by expression”CLCN7“transcriptional regulation”
TFE3“up-regulates quantity by expression”CLCN7“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 153 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Neutrophil degranulation184.6×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

1460 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic39
Likely pathogenic47
Uncertain significance531
Likely benign592
Benign128

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1012215NM_001287.6(CLCN7):c.952T>C (p.Phe318Leu)Pathogenic
1065115NM_001287.6(CLCN7):c.1561G>A (p.Gly521Arg)Pathogenic
1410271NC_000016.9:g.(?1507235)(1524975_?)delPathogenic
1453932NM_001287.6(CLCN7):c.746C>T (p.Pro249Leu)Pathogenic
1458929NM_001287.6(CLCN7):c.718G>A (p.Gly240Arg)Pathogenic
1459594NC_000016.10:g.1457356_1457357insATGCTCAGAGACACGCGTGACGCGGCCCTTCCTGGAGACCAGAAGGACCGPathogenic
1675596NM_001287.6(CLCN7):c.1424dup (p.Ser476fs)Pathogenic
1685637NM_001287.6(CLCN7):c.2066del (p.Lys689fs)Pathogenic
1685638NM_001287.6(CLCN7):c.1562G>C (p.Gly521Ala)Pathogenic
1701268NM_001287.6(CLCN7):c.2053_2072delinsT (p.Ile685fs)Pathogenic
2012245NM_001287.6(CLCN7):c.1612dup (p.Ala538fs)Pathogenic
2014467NM_001287.6(CLCN7):c.2049dup (p.Leu684fs)Pathogenic
2025971NM_001287.6(CLCN7):c.381G>A (p.Trp127Ter)Pathogenic
2036195NM_001287.6(CLCN7):c.512del (p.Gly171fs)Pathogenic
2049877NM_001287.6(CLCN7):c.1147_1148insA (p.Val383fs)Pathogenic
2128622NM_001287.6(CLCN7):c.1270dup (p.Thr424fs)Pathogenic
2137755NM_001287.6(CLCN7):c.869C>T (p.Ser290Phe)Pathogenic
2137756NM_001287.6(CLCN7):c.811C>T (p.Arg271Ter)Pathogenic
2424116NC_000016.9:g.(?1496632)(1524975_?)delPathogenic
2664512NM_001287.6(CLCN7):c.892dup (p.Ser298fs)Pathogenic
2736274NM_001287.6(CLCN7):c.637C>T (p.Leu213Phe)Pathogenic
2840563NM_001287.6(CLCN7):c.282T>G (p.Tyr94Ter)Pathogenic
2846756NM_001287.6(CLCN7):c.259G>T (p.Glu87Ter)Pathogenic
2852015NM_001287.6(CLCN7):c.1331dup (p.Ser445fs)Pathogenic
3243623NC_000016.9:g.(?1524815)(1524975_?)delPathogenic
3721940NM_001287.6(CLCN7):c.2250+1G>APathogenic
3721941NM_001287.6(CLCN7):c.2134C>T (p.Arg712Ter)Pathogenic
372326NM_001287.6(CLCN7):c.2144A>G (p.Tyr715Cys)Pathogenic
3901171NM_001287.6(CLCN7):c.797C>G (p.Ser266Ter)Pathogenic
4688721NM_001287.6(CLCN7):c.1828_1829del (p.Ser610fs)Pathogenic

SpliceAI

5383 predictions. Top by Δscore:

VariantEffectΔscore
16:1447000:GCTCA:Gdonor_loss1.0000
16:1447001:CTCA:Cdonor_loss1.0000
16:1447002:TCA:Tdonor_loss1.0000
16:1447003:CACC:Cdonor_loss1.0000
16:1447005:C:CTdonor_loss1.0000
16:1447082:GCCTC:Gacceptor_gain1.0000
16:1447083:CCTCC:Cacceptor_gain1.0000
16:1447084:CTC:Cacceptor_gain1.0000
16:1447085:TC:Tacceptor_gain1.0000
16:1447085:TCC:Tacceptor_loss1.0000
16:1447086:CC:Cacceptor_gain1.0000
16:1447086:CCT:Cacceptor_loss1.0000
16:1447087:C:CCacceptor_gain1.0000
16:1447091:A:Tacceptor_gain1.0000
16:1447377:ATGC:Adonor_gain1.0000
16:1447424:A:ACdonor_gain1.0000
16:1447425:C:CCdonor_gain1.0000
16:1447448:C:CAdonor_gain1.0000
16:1447456:T:TAdonor_gain1.0000
16:1447564:AACAC:Aacceptor_gain1.0000
16:1447565:ACAC:Aacceptor_gain1.0000
16:1447566:CAC:Cacceptor_gain1.0000
16:1447566:CACC:Cacceptor_gain1.0000
16:1447567:AC:Aacceptor_gain1.0000
16:1447568:CC:Cacceptor_gain1.0000
16:1447568:CCT:Cacceptor_loss1.0000
16:1447569:C:CCacceptor_gain1.0000
16:1447577:G:Tacceptor_gain1.0000
16:1447651:GCAC:Gdonor_loss1.0000
16:1447652:CA:Cdonor_loss1.0000

AlphaMissense

5211 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:1446698:C:AR784M1.000
16:1446710:C:TG780E1.000
16:1447031:A:GL769P1.000
16:1447043:C:TG765D1.000
16:1447665:A:GL688P1.000
16:1447677:A:GL684P1.000
16:1449046:C:GA573P1.000
16:1449057:A:TI569N1.000
16:1449060:A:TV568D1.000
16:1449066:A:GL566P1.000
16:1449068:G:CS565R1.000
16:1449068:G:TS565R1.000
16:1449070:T:GS565R1.000
16:1449278:A:GL556P1.000
16:1449284:G:TA554D1.000
16:1449293:C:TG551E1.000
16:1449294:C:GG551R1.000
16:1449294:C:TG551R1.000
16:1450540:C:TG525D1.000
16:1450541:C:GG525R1.000
16:1450544:A:GW524R1.000
16:1450544:A:TW524R1.000
16:1450552:C:TG521E1.000
16:1450553:C:AG521W1.000
16:1450553:C:GG521R1.000
16:1450553:C:TG521R1.000
16:1450561:A:GL518P1.000
16:1450580:C:AG512W1.000
16:1455757:A:GW319R1.000
16:1455757:A:TW319R1.000

dbSNP variants (sampled 300 via entrez): RS1000097648 (16:1450276 G>A), RS1000174399 (16:1457520 C>T), RS1000196945 (16:1448878 C>CG), RS1000227977 (16:1453690 G>C), RS1000272517 (16:1475598 C>T), RS1000347390 (16:1461124 C>T), RS1000353389 (16:1448724 G>T), RS1000716923 (16:1469195 G>C,T), RS1000729201 (16:1467216 C>G,T), RS1000742672 (16:1473679 C>A), RS1000748555 (16:1469063 G>A,C), RS1000908314 (16:1463456 A>T), RS1000952334 (16:1447539 C>G,T), RS1000965846 (16:1454658 G>A), RS1001180202 (16:1447306 C>A,G,T)

Disease associations

OMIM: gene MIM:602727 | disease phenotypes: MIM:166600, MIM:611490, MIM:618541, MIM:259700, MIM:266920

GenCC curated gene-disease

DiseaseClassificationInheritance
autosomal dominant osteopetrosis 2DefinitiveAutosomal dominant
autosomal recessive osteopetrosis 4DefinitiveAutosomal recessive
hypopigmentation, organomegaly, and delayed myelination and developmentStrongAutosomal dominant
autosomal recessive osteopetrosis 6SupportiveAutosomal recessive
autosomal recessive osteopetrosisSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (3)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
hypopigmentation, organomegaly, and delayed myelination and developmentDefinitiveAD
autosomal dominant osteopetrosis 2DefinitiveAD
autosomal recessive osteopetrosis 4DefinitiveAR

Mondo (9): autosomal dominant osteopetrosis 2 (MONDO:0008156), autosomal recessive osteopetrosis 4 (MONDO:0012676), hypopigmentation, organomegaly, and delayed myelination and development (MONDO:0032805), bone disorder (MONDO:0005381), autosomal recessive osteopetrosis (MONDO:0019026), osteopetrosis (MONDO:0017198), short-rib thoracic dysplasia 9 with or without polydactyly (MONDO:0009964), connective tissue disorder (MONDO:0003900), autosomal recessive osteopetrosis 6 (MONDO:0012679)

Orphanet (5): Albers-Schönberg osteopetrosis (Orphanet:53), Autosomal recessive malignant osteopetrosis (Orphanet:667), Rare bone disease related to a common gene or pathway defect (Orphanet:364803), Osteopetrosis and related disorders (Orphanet:2781), Saldino-Mainzer syndrome (Orphanet:140969)

HPO phenotypes

117 total (30 of 117 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000164Abnormality of the dentition
HP:0000238Hydrocephalus
HP:0000256Macrocephaly
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000365Hearing impairment
HP:0000388Otitis media
HP:0000505Visual impairment
HP:0000543Optic disc pallor
HP:0000572Visual loss
HP:0000618Blindness
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000649Abnormality of visual evoked potentials
HP:0000670Carious teeth
HP:0000684Delayed eruption of teeth
HP:0000689Dental malocclusion
HP:0000707Abnormality of the nervous system
HP:0000772Abnormal rib morphology
HP:0000774Narrow chest
HP:0000944Abnormal metaphysis morphology
HP:0000954Single transverse palmar crease
HP:0000957Cafe-au-lait spot
HP:0000967Petechiae
HP:0000978Bruising susceptibility
HP:0000980Pallor
HP:0001010Hypopigmentation of the skin
HP:0001272Cerebellar atrophy

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010002_107Refractive error6.000000e-18
GCST010481_10Acute anterior uveitis in ankylosing spondylitis1.000000e-06

MeSH disease descriptors (5)

DescriptorNameTree numbers
D001847Bone DiseasesC05.116
D003240Connective Tissue DiseasesC17.300
D010022OsteopetrosisC05.116.099.708.702.678
C566933Osteopetrosis, Autosomal Recessive 4 (supp.)
C566931Osteopetrosis, Autosomal Recessive 6 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: other ic — ClC family

Most potent curated ligand interactions (3 total), top 3:

LigandActionAffinityParameter
DIDSChannel blocker4.4pIC50
NS5818Channel blocker4.3pIC50
NPPBChannel blocker3.8pIC50

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases methylation, increases expression, affects expression3
Ozoneincreases oxidation, increases expression, increases abundance, affects expression, affects cotreatment (+1 more)3
sodium arseniteaffects expression, increases expression2
methacrylaldehydeaffects cotreatment, decreases expression, increases oxidation, increases expression, increases abundance2
apilimodaffects response to substance2
Acroleinaffects cotreatment, decreases expression, increases oxidation, increases expression, increases abundance2
Air Pollutantsaffects cotreatment, decreases expression, increases abundance, increases oxidation, affects expression2
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation, increases expression2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
FR900359affects phosphorylation1
bisphenol Fincreases expression, affects cotreatment1
alpha-pineneaffects cotreatment, decreases expression, increases oxidation, increases abundance1
mono-(2-ethylhexyl)phthalateincreases abundance, increases methylation1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
cobaltous chlorideincreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
cupric chlorideaffects expression1
coumarinincreases phosphorylation1
N,N,N’,N’-tetrakis(2-pyridylmethyl)ethylenediaminedecreases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateincreases expression1
ginsenoside Rb1decreases expression, decreases reaction1
jinfukangaffects cotreatment, increases expression1
MT19c compounddecreases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Sunitinibincreases expression1
alpha-Chlorohydrindecreases expression, decreases reaction1
Atrazinedecreases expression1
Vehicle Emissionsdecreases methylation1

Cellosaurus cell lines

6 cell lines: 4 cancer cell line, 2 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B1NGAbcam HeLa CLCN7 KOCancer cell lineFemale
CVCL_E0ABUbigene HeLa CLCN7 KOCancer cell lineFemale
CVCL_E1DRUbigene U2OS CLCN7 KOCancer cell lineFemale
CVCL_SJ17HAP1 CLCN7 (-)Cancer cell lineMale
CVCL_UM44BIHi002-AInduced pluripotent stem cellMale
CVCL_UM45BIHi002-BInduced pluripotent stem cellMale

Clinical trials (associated diseases)

106 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01042158PHASE4COMPLETEDA Clinical Trial of Ambrisentan and Tadalafil in Pulmonary Arterial Hypertension Associated With Systemic Sclerosis
NCT03688191PHASE4UNKNOWNStudy of Sirolimus in CTD-TP in China
NCT04169100PHASE4UNKNOWNNovel Form of Acquired Long QT Syndrome
NCT04197050PHASE4UNKNOWNEffect of Sacubitril/Valsartan on Reduced Right Ventricular Ejection Fraction in Patients With CTD
NCT04928586PHASE4UNKNOWNImmunosuppressant Combined With Pirfenidone in CTD-ILD
NCT05440240PHASE4RECRUITINGPercutaneous Needle Fasciotomy +/- Corticosteroid Injection for Dupuytren’s Contracture
NCT05505409PHASE4UNKNOWNEfficacy and Safety of Pirfenidone in CTD-ILD
NCT06499233PHASE4RECRUITINGEfficacy and Safety of Prophylactic Treatment for Pneumocystis Jirovecii Pneumonia in Patients With Autoimmune Inflammatory Rheumatic Disease
NCT00004402PHASE3COMPLETEDPhase III Randomized Study of Interferon Gamma in Children With Severe, Congenital Osteopetrosis
NCT00864201PHASE3UNKNOWNA Study to Evaluate the Use of Bosentan in Patients With Exercise Induced Pulmonary Arterial Hypertension Associated With Connective Tissue Disease
NCT01196091PHASE3COMPLETEDA Study of LY2127399 in Participants With Systemic Lupus Erythematosus
NCT01205438PHASE3COMPLETEDA Study of LY2127399 in Participants With Systemic Lupus Erythematosus
NCT01488708PHASE3TERMINATEDOn Open-Label Study in Participants With Systemic Lupus Erythematosus
NCT03626688PHASE3COMPLETEDA Study Evaluating the Efficacy and Safety of Ralinepag to Improve Treatment Outcomes in PAH Patients
NCT03683186PHASE3ENROLLING_BY_INVITATIONA Study Evaluating the Long-Term Efficacy and Safety of Ralinepag in Subjects With PAH Via an Open-Label Extension
NCT04084678PHASE3TERMINATEDA Study of Ralinepag to Evaluate Effects on Exercise Capacity by CPET in Subjects With WHO Group 1 PH
NCT06716606PHASE3RECRUITINGA Study to Investigate the Long-term Safety and Efficacy of Belimumab in Adults With Interstitial Lung Disease (ILD) Associated With Systemic Sclerosis (SSc) and Other Connective Tissue Diseases (CTD) (BLISSconneCTD-OLE)
NCT06917690PHASE3RECRUITINGA Study to Learn About the Safety and Efficacy of the Drug Oleogel-S10 in Japanese Patients With Epidermolysis Bullosa
NCT02584608PHASE2COMPLETEDUse of ACTIMMUNE in Patients With ADO2
NCT00638820PHASE2TERMINATEDReduced Intensity AlloTransplant For Osteopetrosis
NCT00968864PHASE2TERMINATEDT-cell Depleted Alternative Donor Transplantation
NCT02171104PHASE2ACTIVE_NOT_RECRUITINGMT2013-31: Allo HCT for Metabolic Disorders and Severe Osteopetrosis
NCT02666768PHASE2COMPLETEDACTIMMUNE in Intermediate Osteopetrosis
NCT00004357PHASE2COMPLETEDAbsorption of Corticosteroids in Children With Juvenile Dermatomyositis
NCT00005675PHASE2COMPLETEDOral Type I Collagen for Relieving Scleroderma
NCT01808196PHASE2COMPLETEDTesting Effectiveness of Losartan in Patients With EoE With or Without a CTD
NCT02682511PHASE2ACTIVE_NOT_RECRUITINGOral Ifetroban to Treat Diffuse Cutaneous Systemic Sclerosis (SSc) or SSc-associated Pulmonary Arterial Hypertension
NCT04993885PHASE2RECRUITINGAvatrombopag in the Treatment of Adult Immune Thrombocytopenia With Autoantibodies
NCT05516758PHASE2TERMINATEDA Study of Peresolimab (LY3462817) in Participants With Moderately-to-Severely Active Rheumatoid Arthritis
NCT05998759PHASE2RECRUITINGTelitacicept for the Treatment of Connective Tissue Disease-associated Thrombocytopenia
NCT06104228PHASE2RECRUITING129 Xenon MRI as a Biomarker for Diagnosis and Response to Therapy in Pulmonary Arterial Hypertension (PAH)
NCT04525352PHASE1TERMINATEDA Trial to Evaluate Safety and Efficacy of RP-L401-0120 in Subjects With Infantile Malignant Osteopetrosis
NCT00145886PHASE1TERMINATEDrhPTH Therapy for Low Turnover Bone Fragility
NCT01093911PHASE1COMPLETEDSafety Study of CDP7657 in Healthy Volunteers and Patients With Systemic Lupus Erythematosus (SLE)
NCT01764594PHASE1COMPLETEDSafety Study of CDP7657 in Patients With Systemic Lupus Erythematosus
NCT02392130PHASE1COMPLETEDA Clinical Trial to Assess the Potential of LEO 130852A Gel to Reduce Steroid Induced Skin Atrophy on Healthy Skin
NCT03337165PHASE1COMPLETEDAutologous Tolerogenic Dendritic Cells for Treatment of Patients With Rheumatoid Arthritis
NCT03929120PHASE1COMPLETEDAllogeneic Bone Marrow Mesenchymal Stem Cells for Patients With Interstitial Lung Disease (ILD) & Connective Tissue Disorders (CTD)
NCT01166854Not specifiedRECRUITINGCharacterization of Familial Myopathy and Paget Disease of Bone
NCT03527511Not specifiedCOMPLETEDEffect of Active Vitamin D and Etelcalcetide on Human Osteoclasts in Patients With Chronic Kidney Disease