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Gene

CLRN1

clarin 1

Summary

Cytogenetic location
3q25.1
Coordinates
Chromosome 3: 150,926,567–150,972,727 (GRCh38)
Exons
3 exons across 46.2 kb
Protein
232 amino acids
Inheritance
Autosomal recessive
Previous symbols
USH3, USH3A, RP61
MANE Select transcript
ENST00000327047.6NM_174878.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Usher Syndrome

    • Autosomal recessive

      A group of recessive conditions (types 1 to 4) causing sensorineural hearing loss, progressive retinitis pigmentosa and, in some types, balance problems, linked to genes such as USH2A, MYO7A, CDH23, PCDH15, USH1C, USH1G, ADGRV1, WHRN, CLRN1 and ARSG.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      An early diagnosis helps with decisions about the timing of cochlear implants, eye monitoring and eligibility for retinal therapy trials, and is relevant to carrier screening.

Broader groupings

  • Retinitis Pigmentosa

    • One of 77 genes linked to it

      A group of inherited retinal dystrophies with progressive loss of rod and then cone photoreceptors, causing night blindness and gradual loss of peripheral vision.

      • 2 GenCC submitters rate it definitive or strong

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How CLRN1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 3, with a bracket where CLRN1 sits. CLRN1 and 15 genes near it on chromosome 3, from 150,449,647 to 151,449,646.Chromosome 33q25.1p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q29150.6 Mb150.8 Mb151 Mb151.2 Mb151.4 MbTSC22D2: 150,408,241–150,466,422, forward strandTSC22D2SERP1: 150,518,545–150,603,228, reverse strandSERP1EIF2A: 150,546,678–150,586,798, forward strandEIF2ASELENOT: 150,602,875–150,631,370, forward strandSELENOTERICH6: 150,659,885–150,703,971, reverse strandERICH6SIAH2: 150,741,125–150,763,496, reverse strandSIAH2MINDY4B: 150,870,376–150,905,439, reverse strandMINDY4B: 150,882,997–150,941,743, reverse strandCLRN1: 150,926,567–150,972,727, reverse strandCLRN1MED12L: 151,085,286–151,437,072, forward strandMED12LGPR171: 151,197,832–151,203,216, reverse strandGPR171P2RY14: 151,212,115–151,278,811, reverse strandP2RY14GPR87: 151,294,086–151,316,820, reverse strandGPR87P2RY13: 151,326,312–151,329,555, reverse strandP2RY13P2RY12: 151,336,843–151,384,765, reverse strandP2RY12IGSF10: 151,425,384–151,461,186, reverse strandIGSF10Diagram of CLRN1: 3 exons on the reverse strand of chromosome 3Exon 3: 18 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 1: 27 known disease-causing sitesExon 3: 150,926,567–150,928,201, 1,635 basesExon 2: 150,941,582–150,941,761, 180 basesExon 1: 150,972,456–150,972,727, 272 bases3215′3′

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 2.1 kb of the gene's 46.2 kb; 699 of those bases code for the protein.

How a genome test reads CLRN1

58

positions in CLRN1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 46.2 kb of CLRN1, introns included, not only the 2.1 kb of exons.

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

APA

Dante Labs. (n.d.). CLRN1 gene: clarin 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/clrn1

Vancouver

Dante Labs. CLRN1 gene: clarin 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/clrn1

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