Is FOXN1 p.Pro244fs (c.728_729dup) pathogenic?

FOXN1 p.Pro244fs (c.728729dup) is classified Pathogenic in FOXN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-24). No gnomAD frequency available for this variant; Associated with T-cell immunodeficiency, congenital alopecia, and nail dystrophy.

What condition is associated with FOXN1 p.Pro244fs (c.728_729dup)?

FOXN1 p.Pro244fs (c.728_729dup) is associated with T-cell immunodeficiency, congenital alopecia, and nail dystrophy (ClinVar).

How common is FOXN1 p.Pro244fs (c.728_729dup) in the general population?

FOXN1 p.Pro244fs (c.728_729dup) is no gnomAD frequency available for this variant (gnomAD).

FOXN1 p.Pro244fs

Q: How is Severe combined immunodeficiency due to FOXN1 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.728_729dup · rs1597558200 · VCV663245

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

T-cell immunodeficiency, congenital alopecia, and nail dystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 5 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.41	GERP -2.8, phastCons 0.17

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FOXN1
Protein: p.Pro244fs
Coding: c.728_729dup
MANE Select: NM_001369369
dbSNP: rs1597558200
Type: Duplication
Location: chr17:28529120 (GRCh38)
Gene constraint: LOEUF 0.442 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.44 · 2 PDB

Full FOXN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

T-cell immunodeficiency, congenital alopecia, and nail dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Severe combined immunodeficiency due to FOXN1 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

FOXN1 p.Asp313fs Pathogenic ★★★ same condition
FOXN1 p.Gln489fs Pathogenic/Likely pathogenic ★★ same condition
FOXN1 p.Trp363fs Pathogenic ★★ same condition
FOXN1 p.Phe231fs Pathogenic ★ same condition
FOXN1 p.Pro272fs Pathogenic ★ same condition
FOXN1 p.Trp346fs Pathogenic ★ same condition
FOXN1 p.Arg114Ter Pathogenic ★★★ same condition
FOXN1 p.Arg255Ter Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/foxn1-p-pro244fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown