RFWD3 p.Pro74=
c.222G>A · rs746152970 · VCV2194395
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6.9 | GERP -3.1 |
| Overall | ||
| CADD | 1.671 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/59,994 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000682%
11/1,614,082 alleles · very rare
exomes 10/1,461,882 · genomes 1/152,200 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 29,997 |
| South Asian | 0.00329% | 30,365 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| African / African-American | 0.00133% | 74,928 |
| European (non-Finnish) | 0.000339% | 295,012 |
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
- RFWD3
- Protein
- p.Pro74=
- Coding
- c.222G>A
- MANE Select
- NM_018124
- dbSNP
- rs746152970
- Type
- single nucleotide variant
- Location
- chr16:74661228 (GRCh38)
- Gene constraint
- LOEUF 0.931 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.95 · 1 PDB
Similar variants
- RFWD3 p.Pro74Leu Likely benign ★ same residue
- RFWD3 p.Ala22Pro Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala231Pro Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala244Val Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala24Val Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala372Thr Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala447Gly Uncertain significance ★★ ⚠ same type
- RFWD3 p.Ala581Gly Uncertain significance ★★ ⚠ 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/rfwd3-p-pro74 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown