TSEN2 p.Phe339fs
c.1016del · VCV3692161
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 8 of 12 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -4 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- TSEN2
- Protein
- p.Phe339fs
- Coding
- c.1016del
- MANE Select
- NM_025265
- Type
- Deletion
- Location
- chr3:12519113 (GRCh38)
- Gene constraint
- LOEUF 1.212 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 73.63 · 5 PDB
- Residue 339
- an α-helix
Similar variants
- TSEN2 p.Phe339Cys Uncertain significance ★ ⚠ same residue
- TSEN2 c.960+1_960+5del Likely pathogenic ★★ same type
- TSEN2 p.Gln118fs Likely pathogenic ★★ same type
- TSEN2 p.Phe306fs Pathogenic ★★ same type
- TSEN2 c.1248+61del Benign ★★ same type
- TSEN2 p.Arg232fs Likely pathogenic ★ same type
- TSEN2 p.Cys421fs Likely pathogenic ★ same type
- TSEN2 p.Glu264fs Pathogenic ★ same type
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/tsen2-p-phe339fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown