Is RPS24 p.Phe56= (c.168T>C) pathogenic?

RPS24 p.Phe56= (c.168T>C) is classified Benign/Likely benign in RPS24 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-01). Rare (popmax 0.926%, afr); Associated with Diamond-Blackfan anemia 3.

What condition is associated with RPS24 p.Phe56= (c.168T>C)?

RPS24 p.Phe56= (c.168T>C) is associated with Diamond-Blackfan anemia 3, Diamond-Blackfan anemia (ClinVar).

How common is RPS24 p.Phe56= (c.168T>C) in the general population?

RPS24 p.Phe56= (c.168T>C) is rare (popmax 0.926%, afr) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

RPS24 p.Phe56=

c.168T>C · rs57866839 · VCV301092

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

rare (popmax 0.926%, afr)

Conditions

Diamond-Blackfan anemia 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>G here scores Δ0.35 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.6	GERP -1.2, phastCons 1
Overall
CADD	11.12	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.926% African / African-American · 695/75,062 alleles

Filtering AF 0.869% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.846%

Overall 0.0496% 800/1,612,936 alleles · rare exomes 423/1,460,610 · genomes 377/152,326 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.926%	108
Middle Eastern	0.0825%	1,212
Admixed American	0.0733%	1,364
Remaining individualsnot grpmax-eligible	0.0672%	1,488
South Asian	0.0022%	45,538
European (non-Finnish)	0.00102%	98,335

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.Phe56=
Coding: c.168T>C
MANE Select: NM_033022
dbSNP: rs57866839
Type: single nucleotide variant
Location: chr10:78035609 (GRCh38)
Gene constraint: LOEUF 0.182 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 89.04 · 209 PDB
Residue 56: a β-strand

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

Disease context

Diamond-Blackfan anemia 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Diamond-Blackfan anemia

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.Ala220Val 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

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-phe56 (accessed [today's date]).

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