RNF43 p.Ser512=
c.1536C>T · rs748623760 · VCV2173586
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 5.646 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0022%
South Asian · 2/91,086 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000136%
Overall
0.000248%
4/1,613,934 alleles · very rare
exomes 4/1,461,700 · genomes 0/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0022% | 45,543 |
| Admixed American | 0.00167% | 60,012 |
| European (non-Finnish) | 8.48e-05% | 1,179,933 |
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.Ser512=
- Coding
- c.1536C>T
- MANE Select
- NM_017763
- dbSNP
- rs748623760
- Type
- single nucleotide variant
- Location
- chr17:58358240 (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.Ser512Asn 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-ser512 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown