TCF20 p.Ser55fs
c.161dup · rs2518248717 · VCV2698068
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 haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -1.7 |
| Region caveats | ||
| Repeat context | tandem | (CCACTG)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- TCF20
- Protein
- p.Ser55fs
- Coding
- c.161dup
- MANE Select
- NM_001378418
- dbSNP
- rs2518248717
- Type
- Duplication
- Location
- chr22:42215144 (GRCh38)
- Gene constraint
- LOEUF 0.05 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.03
- Residue 55
- the 'disordered' region
Similar variants
- TCF20 p.Ser55del Likely benign ★★ same residue
- TCF20 p.Ser55= Likely benign ★ same residue
- TCF20 p.Asp1029fs Pathogenic ★★ same type
- TCF20 p.Gln122fs Pathogenic ★★ same type
- TCF20 p.Gly857fs Pathogenic/Likely pathogenic ★★ same type
- TCF20 p.Arg1133_Ser1134insArg Uncertain significance ★★ same type
- TCF20 p.Gln320_Gln321insProGlnGln Uncertain significance ★★ same type
- TCF20 p.Gly78_Tyr79insGly Benign/Likely benign ★★ 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/tcf20-p-ser55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown