Gene
CLCN7
Cl-/H+ antiporter 7
- HGNC 2025(opens in a new tab)
- Ensembl gene ENSG00000103249(opens in a new tab)
- NCBI Gene 1186(opens in a new tab)
Summary
- Cytogenetic location
- 16p13.3
- Coordinates
- Chromosome 16: 1,444,935–1,475,028 (GRCh38)
- Exons
- 25 exons across 30.1 kb
- Protein
- 805 amino acids
- Also known as
- CLC-7, OPTA2, CLC7, ClC-7, PPP1R63
- MANE Select transcript
- ENST00000382745.9NM_001287.6
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
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Osteopetrosis
Osteopetrosis, also known as marble bone disease, is a descriptive term that refers to a group of rare, heritable disorders of the skeleton characterized by increased bone density on radiographs.
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
How CLCN7 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 4.2 kb of the gene's 30.1 kb; 2,418 of those bases code for the protein.
How a genome test reads CLCN7
41
positions in CLCN7 where ClinVar classes a change as pathogenic or likely pathogenic
1 of them (2.4%) falls in a region short reads find hard.
- Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
A whole genome covers all 30.1 kb of CLCN7, introns included, not only the 4.2 kb of exons.
Traits linked to CLCN7
The Human Phenotype Ontology lists these as features of the rare conditions CLCN7 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the musculoskeletal system
- Harder, denser, fracture-prone bones
- Increased bone mineral density
- Abnormal shape of end part of bone
- Abnormality of bone mineral density
- Abnormality of the ribs
- Arthritis
- Bone pain
- Death of bone due to decreased blood supply
Show 17 more traits
- Degenerative joint disease
- Increased bone density in skeletal bones
- Joint dislocation
- Low solidness and mass of the bones
- Narrow chest
- Recurrent fractures
- Back pain
- Cortical sclerosis
- Generalized decreased muscle tone
- Increased susceptibility to fractures
- Sandwich appearance of vertebral bodies
- Scoliosis
- Abnormal shape of pelvic girdle bone
- Abnormality of the vertebral endplates
- Hip osteoarthritis
- Recurrent long bone fractures
- Sclerotic vertebral endplates
Abnormality of the nervous system
- Degeneration of cerebellum
- Delayed CNS myelination
- Delayed fine motor development
- Delayed motor skills
- Abnormality of movement
- Cranial nerve paralysis
- Too much cerebrospinal fluid in the brain
- Tremor
Show 2 more traits
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). CLCN7 gene: Cl-/H+ antiporter 7. Retrieved 16 October 2026, from https://dantelabs.com/genes/clcn7
Dante Labs. CLCN7 gene: Cl-/H+ antiporter 7 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/clcn7
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