Is RPS20 p.Pro10= (c.30C>G) pathogenic?

RPS20 p.Pro10= (c.30C>G) is classified Likely benign in RPS20 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-02-27). Very rare (popmax 0.00167%, amr).

How common is RPS20 p.Pro10= (c.30C>G) in the general population?

RPS20 p.Pro10= (c.30C>G) is very rare (popmax 0.00167%, amr) (gnomAD).

RPS20 p.Pro10=

c.30C>G · rs773291256 · VCV1727602

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, 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 -1.2	GERP -4
Overall
CADD	9.435	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,966 alleles

Filtering AF 0.0005% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000366%

Overall 0.000806% 13/1,613,134 alleles · very rare exomes 12/1,461,096 · genomes 1/152,038 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,966
African / African-American	0.00134%	74,888
European (non-Finnish)	0.000932%	107,263

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: RPS20
Protein: p.Pro10=
Coding: c.30C>G
MANE Select: NM_001023
dbSNP: rs773291256
Type: single nucleotide variant
Location: chr8:56074133 (GRCh38)
Gene constraint: LOEUF 0.481 · pLI 0.97 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 85.86 · 194 PDB

Full RPS20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

RPS20 p.Pro10Leu Uncertain significance ★★ ⚠ same residue
RPS20 p.Pro10Ala Uncertain significance ★ ⚠ same residue
RPS20 c.103+5G>A Uncertain significance ★★ same type
RPS20 c.3+5G>A Uncertain significance ★★ same type
RPS20 c.4-4A>G Uncertain significance ★★ same type
RPS20 c.-3G>T Uncertain significance ★★ same type
RPS20 p.Ala119Gly Uncertain significance ★★ ⚠ same type
RPS20 p.Ala16Thr 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/rps20-p-pro10 (accessed [today's date]).

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