Is RPS10 p.Lys24Arg (c.71A>G) pathogenic?

RPS10 p.Lys24Arg (c.71A>G) is classified Conflicting classifications of pathogenicity in RPS10 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-12-29). AlphaMissense: likely benign (0.1791); Rare (popmax 0.152%, sas); Associated with Diamond-Blackfan anemia 9.

What condition is associated with RPS10 p.Lys24Arg (c.71A>G)?

RPS10 p.Lys24Arg (c.71A>G) is associated with Diamond-Blackfan anemia 9, Diamond-Blackfan anemia (ClinVar).

How common is RPS10 p.Lys24Arg (c.71A>G) in the general population?

RPS10 p.Lys24Arg (c.71A>G) is rare (popmax 0.152%, sas) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

What do computational predictors say about RPS10 p.Lys24Arg (c.71A>G)?

AlphaMissense predicts likely benign (score 0.1791) — an in-silico prediction, not a clinical call.

RPS10 p.Lys24Arg

c.71A>G · rs201147592 · VCV356422

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1791 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.152%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Diamond-Blackfan anemia 9

Computational evidence

Protein change
AlphaMissense	0.1791	likely benign
REVEL	0.686	pathogenic-leaning
SaProt	LLR -12.23	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.8	GERP 2, phastCons 1
Regional constraint	o/e 0.62	unconstrained · MANE · 7,712 bp · p 1.1e-08 · regional, not allelic
Overall
CADD	26.9	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.152% South Asian · 138/91,062 alleles

Filtering AF 0.131% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.123%

Overall 0.0258% 417/1,613,810 alleles · rare exomes 401/1,461,552 · genomes 16/152,258 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.152%	660
Ashkenazi Jewishnot grpmax-eligible	0.125%	800
Middle Eastern	0.0851%	1,174
Remaining individualsnot grpmax-eligible	0.0432%	2,314
European (non-Finnish)	0.0168%	5,960
East Asian	0.0111%	8,974
Admixed American	0.00833%	12,003
African / African-American	0.00267%	37,508

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: RPS10
Protein: p.Lys24Arg
Coding: c.71A>G
MANE Select: NM_001014
dbSNP: rs201147592
Type: single nucleotide variant
Location: chr6:34425151 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 75.34 · 195 PDB
Residue 24: a β-strand

Full RPS10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Diamond-Blackfan anemia 9 — 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

RPS10 p.Arg113Ter Pathogenic ★★ same condition
RPS10 c.322+3A>G Uncertain significance ★★ same condition
RPS10 p.Arg158His Uncertain significance ★★ ⚠ same condition
RPS10 p.Arg55Gln Uncertain significance ★★ same condition
RPS10 p.Arg8Trp Uncertain significance ★★ ⚠ same condition
RPS10 p.Arg96Cys Uncertain significance ★★ ⚠ same condition
RPS10 p.Arg98His Uncertain significance ★★ ⚠ same condition
RPS10 p.Asp137Asn 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/rps10-p-lys24arg (accessed [today's date]).

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