Is RPS20 p.Phe3= (c.9T>C) pathogenic?

RPS20 p.Phe3= (c.9T>C) is classified Likely benign in RPS20 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-11). Absent from gnomAD v4.1.

How common is RPS20 p.Phe3= (c.9T>C) in the general population?

RPS20 p.Phe3= (c.9T>C) is absent from gnomAD v4.1 (gnomAD).

RPS20 p.Phe3=

c.9T>C · rs2486985695 · VCV2036634

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 3.8	GERP -0.41, phastCons 1
Overall
CADD	10.71	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: RPS20
Protein: p.Phe3=
Coding: c.9T>C
MANE Select: NM_001023
dbSNP: rs2486985695
Type: single nucleotide variant
Location: chr8:56074154 (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 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
RPS20 p.Ala16Val Uncertain significance ★★ ⚠ same type
RPS20 p.Ala2Gly 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-phe3 (accessed [today's date]).

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