RNF43 p.Val520=
c.1560G>A · rs922213300 · VCV2996370
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 -0.27 | GERP -3.9, phastCons 0.01 |
| Overall | ||
| CADD | 0.207 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,580 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,382 alleles · very rare
exomes 2/1,461,192 · genomes 0/152,190 · 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
- RNF43
- Protein
- p.Val520=
- Coding
- c.1560G>A
- MANE Select
- NM_017763
- dbSNP
- rs922213300
- Type
- single nucleotide variant
- Location
- chr17:58358216 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.86 · 2 PDB
- Residue 520
- the 'disordered' region
Similar variants
- RNF43 p.Val520Gly 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-val520 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown