Gene
OPHN1
oligophrenin 1
- HGNC 8148(opens in a new tab)
- Ensembl gene ENSG00000079482(opens in a new tab)
- NCBI Gene 4983(opens in a new tab)
Summary
- Cytogenetic location
- Xq12
- Coordinates
- Chromosome X: 68,042,344–68,433,495 (GRCh38)
- Exons
- 25 exons across 391.2 kb
- Protein
- 802 amino acids
- Also known as
- OPN1, ARHGAP41
- Previous symbols
- MRX60
- MANE Select transcript
- ENST00000355520.6NM_002547.3
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Intellectual Disability
One of 233 genes linked to it
- ClinGen rates the link definitive
- 5 GenCC submitters rate it definitive or strong
How OPHN1 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 7.6 kb of the gene's 391.2 kb; 2,409 of those bases code for the protein.
How a genome test reads OPHN1
37
positions in OPHN1 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 391.2 kb of OPHN1, introns included, not only the 7.6 kb of exons.
Traits linked to OPHN1
The Human Phenotype Ontology lists these as features of the rare conditions OPHN1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of the nervous system
- Global developmental delay
- Intellectual disability
- Cerebellar vermis hypoplasia
- Small cerebellum
- Ventriculomegaly
- Abnormal speech pattern
- Ataxia
- Autism spectrum disorder
Show 26 more traits
- Delayed ability to sit
- Focal impaired awareness seizure
- Generalized myoclonic seizure
- Intellectual disability, severe
- IQ between 34 and 49
- Partial absence of cerebellar vermis
- Poor eye contact
- Poor social interactions
- Poor speech
- Absent speech development
- Aplasia/Hypoplasia of the cerebellar vermis
- Attention deficit
- Balance impairment
- Caudate atrophy
- Delayed ability to walk
- Disorganization of the anterior cerebellar vermis
- Frontal cortical atrophy
- Intention tremor
- Low frustration tolerance
- Repetitive movements
- Retrocerebellar cyst
- Self-mutilation
- Temporal cortical atrophy
- Epilepsy
- Inability to coordinate movements when walking
- More active than typical
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.). OPHN1 gene: oligophrenin 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/ophn1
Dante Labs. OPHN1 gene: oligophrenin 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ophn1
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