RNF43 p.Arg439=
c.1317G>A · rs767663775 · VCV1139097
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, 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 1.1 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 6.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/59,994 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00632%
102/1,613,702 alleles · ultra-rare
exomes 95/1,461,498 · genomes 7/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,666 |
| European (non-Finnish) | 0.00754% | 13,257 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,238 |
| Finnishnot grpmax-eligible | 0.00156% | 63,914 |
| African / African-American | 0.00133% | 74,926 |
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
- RNF43
- Protein
- p.Arg439=
- Coding
- c.1317G>A
- MANE Select
- NM_017763
- dbSNP
- rs767663775
- Type
- single nucleotide variant
- Location
- chr17:58358459 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.86 · 2 PDB
- Residue 439
- the 'disordered' region
Similar variants
- RNF43 p.Arg439Ser Uncertain significance ★ ⚠ same residue
- RNF43 p.Arg337Ter Pathogenic/Likely pathogenic ★★ same type
- RNF43 c.252+2C>G Uncertain significance ★★ same type
- RNF43 c.687+5G>T Uncertain significance ★★ same type
- RNF43 c.688-3C>T Uncertain significance ★★ same type
- RNF43 p.Ala115Asp Uncertain significance ★★ ⚠ same type
- RNF43 p.Ala115Val Uncertain significance ★★ ⚠ same type
- RNF43 p.Ala123Thr 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/rnf43-p-arg439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown