Variant
FOXN1 C82X
NM_001369369.1(FOXN1):c.246C>A (p.Cys82Ter)
- p.Cys82Ter
- p.C82*
- rs2508354964
- ClinVar classification
- Pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 27 September 2024
- Expert panel
- ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
C82X is a nonsense variant in FOXN1: it creates an early stop signal, so the protein the gene encodes is predicted to be cut short. ClinVar classifies it as pathogenic for T-cell immunodeficiency, congenital alopecia, and nail dystrophy (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| T-cell immunodeficiency, congenital alopecia, and nail dystrophyClinVar VCV002780381 (opens in a new tab) | Pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 27 September 2024 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Where it lies in FOXN1
C82X lies in exon 3 of the 9 in FOXN1's MANE Select transcript, NM_001369369.1.
Molecular details
| Gene | FOXN1 |
|---|---|
| Transcript | NM_001369369.1MANE Select |
| Coding DNA change (HGVS c.) | c.246C>A |
| Protein change (HGVS p.) | p.Cys82Terp.C82* |
| Predicted consequence | Nonsense (stop gained)stop_gained (opens in a new tab) |
| Predicted impact | High |
| Position (GRCh38) | chr17:28524625 C>A |
| Position (GRCh37) | chr17:26851643 C>A |
| dbSNP ID | rs2508354964 (opens in a new tab) |
| ClinVar Variation ID | VCV002780381 (opens in a new tab) |
| ClinVar Allele ID | 2944121 |
| ClinGen Allele Registry ID | CA398320910 (opens in a new tab) |
| ClinVar name | NM_001369369.1(FOXN1):c.246C>A (p.Cys82Ter) |
FOXN1 C82X in other databases
Reports that look at this variant (2)
These Genome Test condition reports include C82X among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Other Inborn Errors of Immunity | Immunodeficiency Disease | |
| Severe Combined Immunodeficiency | Severe Combined Immunodeficiency | Autosomal recessive |
Other variants in FOXN1
- D313Tfs*169Pathogenic3 stars out of 4
- E303Sfs*247Likely pathogenic3 stars out of 4
- E390Kfs*160Likely pathogenic3 stars out of 4
- G337Efs*213Likely pathogenic3 stars out of 4
- H321RLikely pathogenic3 stars out of 4
- H457Pfs*93Pathogenic3 stars out of 4
- I433Ffs*117Likely pathogenic3 stars out of 4
- L325PLikely pathogenic3 stars out of 4
- L426Tfs*123Likely pathogenic3 stars out of 4
- L439Cfs*111Likely pathogenic3 stars out of 4
Limitations
This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant.
Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports.
Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements.
If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor.
Sources & credits
- Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information.
- Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0.
- Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16).
- Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- Difficult regions from the Genome in a Bottle Consortium (release v3.6).
- Transcripts from MANE (release v1.5), NCBI and EMBL-EBI.
- Predicted consequences from mehari (release 0.11.0), with transcript models from cdot.
- Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). FOXN1 C82X (c.246C>A, rs2508354964) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/foxn1/variants/c82x
Dante Labs. FOXN1 C82X (c.246C>A, rs2508354964) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/foxn1/variants/c82x
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