TCF20 p.Val352=
c.1056T>C · rs142522528 · VCV731819
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.866%, afr)
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 -0.43 | GERP -2.8 |
| Overall | ||
| CADD | 3.655 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.866%
African / African-American · 650/75,054 alleles
Filtering AF
0.811%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.789%
Overall
0.046%
743/1,614,204 alleles · rare
exomes 396/1,461,892 · genomes 347/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.866% | 115 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,953 |
| Middle Eastern | 0.0495% | 2,021 |
| Admixed American | 0.0283% | 3,530 |
| European (non-Finnish) | 0.00339% | 29,501 |
| South Asian | 0.0011% | 91,090 |
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.Val352=
- Coding
- c.1056T>C
- MANE Select
- NM_001378418
- dbSNP
- rs142522528
- Type
- single nucleotide variant
- Location
- chr22:42214250 (GRCh38)
- Gene constraint
- LOEUF 0.05 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.03
- Residue 352
- 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-val352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown