Is RPS24 p.Pro52= (c.156G>T) pathogenic?

RPS24 p.Pro52= (c.156G>T) is classified Likely benign in RPS24 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-29). Very rare (popmax 0.000254%, nfe); Associated with Diamond-Blackfan anemia.

What condition is associated with RPS24 p.Pro52= (c.156G>T)?

RPS24 p.Pro52= (c.156G>T) is associated with Diamond-Blackfan anemia (ClinVar).

How common is RPS24 p.Pro52= (c.156G>T) in the general population?

RPS24 p.Pro52= (c.156G>T) is very rare (popmax 0.000254%, nfe) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

RPS24 p.Pro52=

c.156G>T · rs150157180 · VCV1646291

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

Diamond-Blackfan anemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -0.28	GERP -4.3, phastCons 0.002
Overall
CADD	6.414	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,180,018 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,613,404 alleles · very rare exomes 3/1,461,146 · genomes 0/152,258 · joint denominator

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: RPS24
Protein: p.Pro52=
Coding: c.156G>T
MANE Select: NM_033022
dbSNP: rs150157180
Type: single nucleotide variant
Location: chr10:78035597 (GRCh38)
Gene constraint: LOEUF 0.182 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.04 · 209 PDB
Residue 52: an α-helix

Full RPS24 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Diamond-Blackfan anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Diamond-Blackfan anemia (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

RPS24 p.Pro52Gln Uncertain significance ★ ⚠ same residue
RPS24 p.Pro52Leu Uncertain significance ★ ⚠ same residue
RPS24 p.Arg16Ter Pathogenic ★★ same condition
RPS24 c.390+4T>C Uncertain significance ★★ same condition
RPS24 c.4-3C>T Uncertain significance ★★ same condition
RPS24 p.Arg41Gln Uncertain significance ★★ ⚠ same condition
RPS24 p.Arg8His Uncertain significance ★★ ⚠ same condition
RPS24 p.Gly31Arg 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/rps24-p-pro52 (accessed [today's date]).

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