TCF20 p.Arg447=
c.1339C>A · rs550035576 · VCV2060573
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0022%, sas)
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 8.6 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 9.314 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,084 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000124%
2/1,614,174 alleles · very rare
exomes 2/1,461,894 · genomes 0/152,280 · joint denominator
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.Arg447=
- Coding
- c.1339C>A
- MANE Select
- NM_001378418
- dbSNP
- rs550035576
- Type
- single nucleotide variant
- Location
- chr22:42213967 (GRCh38)
- Gene constraint
- LOEUF 0.05 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 39.03
- Residue 447
- a UniProt-annotated variant site (in ddviba)
Similar variants
- TCF20 p.Arg447Gln Benign/Likely benign ★★ 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-arg447 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown