Is RPS10 p.Ala115= (c.345G>A) pathogenic?

RPS10 p.Ala115= (c.345G>A) is classified Likely benign in RPS10 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-05-07). Ultra-rare (popmax 0.0165%, mid); Associated with Diamond-Blackfan anemia.

What condition is associated with RPS10 p.Ala115= (c.345G>A)?

RPS10 p.Ala115= (c.345G>A) is associated with Diamond-Blackfan anemia (ClinVar).

How common is RPS10 p.Ala115= (c.345G>A) in the general population?

RPS10 p.Ala115= (c.345G>A) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

RPS10 p.Ala115=

c.345G>A · rs141996004 · VCV2882894

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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 -1.2	GERP -1.6, phastCons 0.002
Overall
CADD	10.69	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,078 alleles

Filtering AF 0.00175% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00104%

Overall 0.000806% 13/1,613,820 alleles · ultra-rare exomes 9/1,461,666 · genomes 4/152,154 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,078
African / African-American	0.00534%	18,726
South Asian	0.00329%	30,359
Remaining individualsnot grpmax-eligible	0.0016%	62,472
European (non-Finnish)	0.000339%	294,966

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.Ala115=
Coding: c.345G>A
MANE Select: NM_001014
dbSNP: rs141996004
Type: single nucleotide variant
Location: chr6:34421785 (GRCh38)
Gene constraint: LOEUF 0.265 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 75.34 · 195 PDB
Residue 115: the 'disordered' region

Full RPS10 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

RPS10 p.Ala115Val Uncertain significance ★ ⚠ same residue
RPS10-NUDT3 p.Ala115Glu Uncertain significance ★ ⚠ same residue
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.Arg98His 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-ala115 (accessed [today's date]).

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