UNC13D p.Phe242=
c.726T>C · rs2064940432 · VCV2784403
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
familial hemophagocytic lymphohistiocytosis 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.29 | phastCons 0.56 |
| Overall | ||
| CADD | 7.788 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- UNC13D
- Protein
- p.Phe242=
- Coding
- c.726T>C
- MANE Select
- NM_199242
- dbSNP
- rs2064940432
- Type
- single nucleotide variant
- Location
- chr17:75840534 (GRCh38)
- Gene constraint
- LOEUF 0.923 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.04 · 1 PDB
- Residue 242
- the 'interaction with rab27a' region
Disease context
familial hemophagocytic lymphohistiocytosis 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial hemophagocytic lymphohistiocytosis (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Infancy
- Prevalence
- 1-9 / 100 000 (Sweden)
Similar variants
- UNC13D c.1055+1G>A Pathogenic/Likely pathogenic ★★ same condition
- UNC13D c.118-307G>A Pathogenic ★★ same condition
- UNC13D c.118-308C>T Pathogenic/Likely pathogenic ★★ same condition
- UNC13D c.1389+1G>A Pathogenic ★★ same condition
- UNC13D c.1596+1G>C Pathogenic ★★ same condition
- UNC13D c.1727+1G>A Pathogenic/Likely pathogenic ★★ same condition
- UNC13D c.1848+1G>A Pathogenic/Likely pathogenic ★★ same condition
- UNC13D c.2447+2T>C Likely 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/unc13d-p-phe242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown