Is RNF43 p.Pro154= (c.462G>A) pathogenic?

RNF43 p.Pro154= (c.462G>A) is classified Benign/Likely benign in RNF43 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-06-30). Ultra-rare (popmax 0.0493%, afr); Associated with sessile serrated polyposis cancer syndrome.

What condition is associated with RNF43 p.Pro154= (c.462G>A)?

RNF43 p.Pro154= (c.462G>A) is associated with sessile serrated polyposis cancer syndrome (ClinVar).

How common is RNF43 p.Pro154= (c.462G>A) in the general population?

RNF43 p.Pro154= (c.462G>A) is ultra-rare (popmax 0.0493%, afr) (gnomAD).

How is Serrated polyposis syndrome inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

RNF43 p.Pro154=

c.462G>A · rs144994226 · VCV1085885

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0493%, afr)

Conditions

sessile serrated polyposis cancer syndrome

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 -0.54	GERP -4.1, phastCons 0.002
Overall
CADD	7.929	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0493% African / African-American · 37/75,042 alleles

Filtering AF 0.0368% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0323%

Overall 0.00316% 51/1,614,164 alleles · ultra-rare exomes 30/1,461,854 · genomes 21/152,310 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0493%	2,028
Admixed American	0.01%	10,003
Remaining individualsnot grpmax-eligible	0.008%	12,502
European (non-Finnish)	0.000254%	393,338

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.Pro154=
Coding: c.462G>A
MANE Select: NM_017763
dbSNP: rs144994226
Type: single nucleotide variant
Location: chr17:58363395 (GRCh38)
Gene constraint: LOEUF 0.632 · pLI <0.01 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 55.86 · 2 PDB

Full RNF43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

sessile serrated polyposis cancer syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Serrated polyposis syndrome (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial, Unknown
Onset: Adult, Elderly
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

RNF43 p.Pro154Leu Uncertain significance ★★ ⚠ same residue
RNF43 p.Arg337Ter Pathogenic/Likely pathogenic ★★ same condition
RNF43 c.688-3C>T Uncertain significance ★★ same condition
RNF43 p.Ala115Val Uncertain significance ★★ ⚠ same condition
RNF43 p.Ala126Val Uncertain significance ★★ ⚠ same condition
RNF43 p.Ala148Gly Uncertain significance ★★ ⚠ same condition
RNF43 p.Ala169Ser Uncertain significance ★★ ⚠ same condition
RNF43 p.Ala193Val Uncertain significance ★★ ⚠ same condition

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-pro154 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown