Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome: genes and variants
Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome is linked to 1 analyzed protein (KMT2D). 6 DNA variants are known to cause it; 354 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome
KMT2D: Histone-lysine N-methyltransferase 2D
It deposits enhancer-associated H3K4 methylation and coordinates developmental gene expression through chromatin regulatory complexes. Heterozygous loss-of-function variants are a major cause of Kabuki syndrome, and somatic mutations are common in several lymphomas and solid tumors.
6 disease-causing and 354 uncertain variants in KMT2D are linked to Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome.
Known disease-causing variants in Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| KMT2D A3541P | 3541 | Disease-causing (★★) | |
| KMT2D L3528V | 3528 | Disease-causing (★) | |
| KMT2D E3569G | 3569 | Coiled coil | Disease-causing (★) |
| KMT2D R5030L | 5030 | C2HC pre-PHD-type 2 | Disease-causing (★) |
| KMT2D L3542P | 3542 | Disease-causing | |
| KMT2D G3553V | 3553 | Disease-causing |
Same protein, different disease
- Kabuki syndrome is also caused by KMT2D variants; they fall mostly in different places as the Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome variants (34 disease-causing).
Diseases related to Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome
- Kabuki syndrome, also linked to KMT2D
- Medulloblastoma, also linked to KMT2D
Frequently asked questions
Which genes are linked to Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome?
In CATVariant, Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome is linked to 1 analyzed protein: KMT2D (Histone-lysine N-methyltransferase 2D).
How many genetic variants are linked to Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome?
387 variants: 6 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 354 are of uncertain significance or have conflicting reports.
Which uncertain variants in Choanal atresia-athelia-hypothyroidism-delayed puberty-short stature syndrome look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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