Is RPS24 p.Pro30= (c.90C>T) pathogenic?

RPS24 p.Pro30= (c.90C>T) is classified Likely benign in RPS24 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-23). Ultra-rare (popmax 0.0454%, afr); Associated with Diamond-Blackfan anemia.

What condition is associated with RPS24 p.Pro30= (c.90C>T)?

RPS24 p.Pro30= (c.90C>T) is associated with Diamond-Blackfan anemia (ClinVar).

How common is RPS24 p.Pro30= (c.90C>T) in the general population?

RPS24 p.Pro30= (c.90C>T) is ultra-rare (popmax 0.0454%, afr) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

RPS24 p.Pro30=

c.90C>T · rs372043585 · VCV1123867

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0454%, afr)

Conditions

Diamond-Blackfan anemia

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 -1.9	GERP -4.3
Overall
CADD	11.5	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0454% African / African-American · 34/74,896 alleles

Filtering AF 0.0334% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0292%

Overall 0.00403% 65/1,613,912 alleles · ultra-rare exomes 41/1,461,816 · genomes 24/152,096 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0454%	2,203
Remaining individualsnot grpmax-eligible	0.0048%	20,828
East Asian	0.00223%	44,880
European (non-Finnish)	0.00212%	47,199
Admixed American	0.00167%	59,980
Finnishnot grpmax-eligible	0.00156%	64,016

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.Pro30=
Coding: c.90C>T
MANE Select: NM_033022
dbSNP: rs372043585
Type: single nucleotide variant
Location: chr10:78035531 (GRCh38)
Gene constraint: LOEUF 0.182 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.04 · 209 PDB
Residue 30: a β-strand

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.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
RPS24 p.Ile7Ser Uncertain significance ★★ ⚠ same condition
RPS24 p.Leu28Phe 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-pro30 (accessed [today's date]).

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