Is RAD51 p.Arg96= (c.288G>A) pathogenic?

RAD51 p.Arg96= (c.288G>A) is classified Likely benign in RAD51 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-23). Ultra-rare (popmax 0.0187%, sas); Associated with Inborn genetic diseases.

What condition is associated with RAD51 p.Arg96= (c.288G>A)?

RAD51 p.Arg96= (c.288G>A) is associated with Inborn genetic diseases (ClinVar).

How common is RAD51 p.Arg96= (c.288G>A) in the general population?

RAD51 p.Arg96= (c.288G>A) is ultra-rare (popmax 0.0187%, sas) (gnomAD).

RAD51 p.Arg96=

c.288G>A · rs770504390 · VCV1797279

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -1.2	GERP -3.1
Overall
CADD	1.321	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% South Asian · 17/91,084 alleles

Filtering AF 0.0118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00976%

Overall 0.00124% 20/1,614,154 alleles · ultra-rare exomes 20/1,461,868 · genomes 0/152,286 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0187%	5,358
Remaining individualsnot grpmax-eligible	0.0048%	20,836

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: RAD51
Protein: p.Arg96=
Coding: c.288G>A
MANE Select: NM_002875
dbSNP: rs770504390
Type: single nucleotide variant
Location: chr15:40706239 (GRCh38)
Gene constraint: LOEUF 0.467 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 91.59 · 52 PDB
Residue 96: an α-helix

Full RAD51 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RAD51 p.Arg96Gln Uncertain significance ★★ ⚠ same residue
RAD51 p.Arg96Trp Uncertain significance ★ ⚠ same residue
RAD51 p.Ala157Thr Uncertain significance ★★ ⚠ same condition
RAD51 p.Ala209Thr Uncertain significance ★★ same condition
RAD51 p.Ala256Thr Uncertain significance ★★ ⚠ same condition
RAD51 p.Ala328Ser Uncertain significance ★★ ⚠ same condition
RAD51 p.Ala79Val Uncertain significance ★★ ⚠ same condition
RAD51 p.Arg130Gly 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/rad51-p-arg96 (accessed [today's date]).

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