TCF20 p.Pro339=
c.1017C>T · VCV4804847
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0379%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.59 | GERP -0.61, phastCons 1 |
| Overall | ||
| CADD | 6.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0379%
East Asian · 17/44,904 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.0013%
21/1,614,082 alleles · ultra-rare
exomes 19/1,461,892 · genomes 2/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0379% | 2,641 |
| African / African-American | 0.004% | 24,976 |
| European (non-Finnish) | 8.47e-05% | 1,180,043 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- TCF20
- Protein
- p.Pro339=
- Coding
- c.1017C>T
- MANE Select
- NM_001378418
- Type
- single nucleotide variant
- Location
- chr22:42214289 (GRCh38)
- Gene constraint
- LOEUF 0.05 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.03
- Residue 339
- a UniProt-annotated variant site (in ddviba)
Similar variants
- TCF20 p.Arg1907Ter Pathogenic ★★ same type
- TCF20 p.Arg742Ter Pathogenic ★★ same type
- TCF20 p.Gln1082Ter Pathogenic/Likely pathogenic ★★ same type
- TCF20 p.Gln471Ter Pathogenic ★★ same type
- TCF20 p.Gln754Ter Pathogenic ★★ same type
- TCF20 p.Gln935Ter Pathogenic ★★ same type
- TCF20 p.Trp1861Ter Pathogenic/Likely pathogenic ★★ same type
- TCF20 p.Tyr264Ter 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/tcf20-p-pro339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown