Is RPS10 p.Leu2= (c.6G>A) pathogenic?

RPS10 p.Leu2= (c.6G>A) is classified Benign/Likely benign in RPS10 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-26). Rare (popmax 0.466%, eas); Associated with Diamond-Blackfan anemia 9.

What condition is associated with RPS10 p.Leu2= (c.6G>A)?

RPS10 p.Leu2= (c.6G>A) is associated with Diamond-Blackfan anemia 9, Diamond-Blackfan anemia (ClinVar).

How common is RPS10 p.Leu2= (c.6G>A) in the general population?

RPS10 p.Leu2= (c.6G>A) is rare (popmax 0.466%, eas) (gnomAD).

How is Diamond-Blackfan anemia inherited?

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

RPS10 p.Leu2=

c.6G>A · rs146246722 · VCV356423

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.466%, eas)

Conditions

Diamond-Blackfan anemia 9

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 4	GERP 1, phastCons 1
Overall
CADD	15.18	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.466% East Asian · 209/44,826 alleles

Filtering AF 0.414% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.394%

Overall 0.0491% 790/1,608,702 alleles · rare exomes 688/1,456,440 · genomes 102/152,262 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.466%	214
Finnishnot grpmax-eligible	0.392%	255
Remaining individualsnot grpmax-eligible	0.0561%	1,782
European (non-Finnish)	0.024%	4,161
Middle Eastern	0.0165%	6,060
South Asian	0.0111%	9,040
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,472
Admixed American	0.00339%	29,511
African / African-American	0.00267%	37,489

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.Leu2=
Coding: c.6G>A
MANE Select: NM_001014
dbSNP: rs146246722
Type: single nucleotide variant
Location: chr6:34425216 (GRCh38)

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)

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-leu2 (accessed [today's date]).

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