Is RAD51C p.Ser79= (c.237T>A) pathogenic?

RAD51C p.Ser79= (c.237T>A) is classified Likely benign in RAD51C (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-12). Very rare (popmax 8.47e-05%, nfe); Associated with Fanconi anemia complementation group O.

What condition is associated with RAD51C p.Ser79= (c.237T>A)?

RAD51C p.Ser79= (c.237T>A) is associated with Fanconi anemia complementation group O (ClinVar).

How common is RAD51C p.Ser79= (c.237T>A) in the general population?

RAD51C p.Ser79= (c.237T>A) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

RAD51C p.Ser79=

c.237T>A · rs1555593575 · VCV2742819

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

Fanconi anemia complementation group O

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 0.82	GERP -2.5, phastCons 1
Overall
CADD	10.78	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,179,974 alleles

Overall 6.2e-05% 1/1,614,068 alleles · very rare exomes 1/1,461,812 · genomes 0/152,256 · joint denominator

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: RAD51C
Protein: p.Ser79=
Coding: c.237T>A
MANE Select: NM_058216
dbSNP: rs1555593575
Type: single nucleotide variant
Location: chr17:58695022 (GRCh38)
Gene constraint: LOEUF 1.139 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 84.23 · 17 PDB
Residue 79: the 'required for holliday junction resolution activity' region; the 'interaction with rad51b, rad51d and xrcc3' region

Full RAD51C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Fanconi anemia complementation group O — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

RAD51C p.Ser79Ala Uncertain significance ★ ⚠ same residue
RAD51C p.Ser79Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
RAD51C p.Ser79Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
RAD51C p.Ser79Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
RAD51C p.Ser79Pro Benign ★ same residue
RAD51C c.145+1G>A Pathogenic/Likely pathogenic ★★ same condition
RAD51C c.145+1G>T Pathogenic/Likely pathogenic ★★ same condition
RAD51C c.146-1G>A Likely pathogenic ★★ 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/rad51c-p-ser79 (accessed [today's date]).

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