RNF43 c.252+2C>G
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | Δ0.74 | donor loss, 2 bp away · masked 0 · deltas |
| Pangolin | Δ0.52 | loss · gain 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 8.3 | GERP 0.36, phastCons 1 |
| Non-coding constraint | Z 2.08 | 1 kb window · o/e 0.85 · regional · uncalibrated |
| Overall | ||
| CADD | 23.8 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
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
- Coding
- c.252+2C>G
- MANE Select
- NM_017763
- Type
- single nucleotide variant
- Location
- chr17:58415324 (GRCh38)
- Gene constraint
- LOEUF 0.632 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
- Structure
- AlphaFold pLDDT 55.86 · 2 PDB
Similar variants
- RNF43 p.Arg337Ter Pathogenic/Likely pathogenic ★★ 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
- RNF43 p.Ala126Gly Uncertain significance ★★ ⚠ same type
- RNF43 p.Ala126Val 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-c-252-plus-2c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown