FOXN2
Chr 2forkhead box N2
Also known as: HTLF
The encoded protein is a forkhead domain transcription factor that binds to purine-rich DNA sequences and regulates gene transcription. Mutations cause autosomal recessive intellectual disability with speech delay and behavioral abnormalities. This gene is highly constrained against loss-of-function variants, suggesting that complete loss of protein function is likely pathogenic.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Tolerant to missense variation
ClinVar Variant Classifications
98 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 10 | 0 | 10 |
Likely Pathogenic | 0 | 0 | 3 | 0 | 3 |
VUS | 1 | 64 | 5 | 0 | 70 |
Likely Benign | 0 | 2 | 0 | 0 | 2 |
Benign | 0 | 0 | 1 | 2 | 3 |
| Total | 1 | 66 | 19 | 2 | 88 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
FOXN2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools