TCF20 p.Arg1024=
c.3072A>G · rs557229114 · VCV1879563
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0131%, nfe)
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 0.32 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 8.449 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0131%
European (non-Finnish) · 155/1,180,050 alleles
Filtering AF
0.0114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0107%
Overall
0.0103%
166/1,614,104 alleles · ultra-rare
exomes 159/1,461,894 · genomes 7/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0131% | 7,613 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.00534% | 18,734 |
| 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.Arg1024=
- Coding
- c.3072A>G
- MANE Select
- NM_001378418
- dbSNP
- rs557229114
- Type
- single nucleotide variant
- Location
- chr22:42212234 (GRCh38)
- Gene constraint
- LOEUF 0.05 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.03
- Residue 1024
- a UniProt-annotated variant site (in ddviba); a modified residue (omega-n-methylarginine); the 'disordered' region
Similar variants
- TCF20 p.Arg1024Thr Uncertain significance ★ ⚠ same residue
- 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
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-arg1024 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown