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Any syndromic disease characterized by severe hypoplasia of the nose and eyes, palatal abnormalities, deficient taste and smell, inguinal hernias, hypogonadotropic hypogonadism with cryptorchidism, and normal intelligence that occurs due to variation in the SMCHD1 gene.
Features include common findings: Hypogonadotropic hypogonadism, High palate, Midface retrusion, and Paranasal sinus hypoplasia and others; and sometimes findings: Inguinal hernia, Cleft lip, Cataract, and Hypoplastic labia majora and others. 28 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Head and neck | 3 | Cleft lip, High palate, Cleft palate |
Hormones | 2 | Hypogonadotropic hypogonadism, Primary amenorrhea |
Eyes | 1 | Cataract |
Brain and nerves | 1 | Intellectual disability |
Ears | 1 | Conductive hearing impairment |
Age of onset: at birth.
SMCHD1 function has not been fully characterized.
Arhinia, choanal atresia, and microphthalmia is caused by mutations in the SMCHD1 gene on chromosome 18.
Genetic testing for SMCHD1 is available. Testing is considered confirmatory for diagnosis.
Phenotype severity distribution: 6 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
No clinical trials have been registered for arhinia, choanal atresia, and microphthalmia.
9 publications have been identified in PubMed for arhinia, choanal atresia, and microphthalmia. Research spans Case Report / Case Series (44%), Review / Meta-Analysis (33%), and Basic Science / Preclinical (22%).
Rao VV (2026). [PMID: 41962546](https://pubmed.ncbi.nlm.nih.gov/41962546/). *Stem Cell Reports*. [Basic Science / Preclinical]
Xiao LC (2026). [PMID: 41871882](https://pubmed.ncbi.nlm.nih.gov/41871882/). *Genome research*. [Basic Science / Preclinical]
Russo M (2025). [PMID: 40038803](https://pubmed.ncbi.nlm.nih.gov/40038803/). *Italian journal of pediatrics*. [Review / Meta-Analysis]
Patterson KJK (2025). [PMID: 40598710](https://pubmed.ncbi.nlm.nih.gov/40598710/). *American journal of medical genetics. Part A*. [Review / Meta-Analysis]
Pasca L (2025). [PMID: 40181463](https://pubmed.ncbi.nlm.nih.gov/40181463/). *Orphanet journal of rare diseases*. [Review / Meta-Analysis]
Lin LY (2024). [PMID: 38776158](https://pubmed.ncbi.nlm.nih.gov/38776158/). *Ophthalmic plastic and reconstructive surgery*. [Case Report / Case Series]
Yang JL (2024). [PMID: 38773541](https://pubmed.ncbi.nlm.nih.gov/38773541/). *BMC medical genomics*. [Case Report / Case Series]
Kokitsu-Nakata NM (2024). [PMID: 38808953](https://pubmed.ncbi.nlm.nih.gov/38808953/). *American journal of medical genetics. Part A*. [Case Report / Case Series]
Bezerra LL (2024). [PMID: 39365446](https://pubmed.ncbi.nlm.nih.gov/39365446/). *Pediatric radiology*. [Case Report / Case Series]
Data assembled from 7 of 12 sources · Last updated Sep 20, 2026, 5:34 PM UTC
Online Mendelian Inheritance in Man
European rare disease database