Is XRCC2 p.Cys2= (c.6T>C) pathogenic?

XRCC2 p.Cys2= (c.6T>C) is classified Likely benign in XRCC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-23). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with XRCC2 p.Cys2= (c.6T>C)?

XRCC2 p.Cys2= (c.6T>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is XRCC2 p.Cys2= (c.6T>C) in the general population?

XRCC2 p.Cys2= (c.6T>C) is absent from gnomAD v4.1 (gnomAD).

XRCC2 p.Cys2=

c.6T>C · rs2485915708 · VCV3224692

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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 0.63	GERP -3.1, phastCons 0.98
Overall
CADD	11.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: XRCC2
Protein: p.Cys2=
Coding: c.6T>C
MANE Select: NM_005431
dbSNP: rs2485915708
Type: single nucleotide variant
Location: chr7:152676074 (GRCh38)
Gene constraint: LOEUF 1.209 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.57 · 16 PDB

Full XRCC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

XRCC2 c.39+5G>C Uncertain significance ★★ same condition
XRCC2 p.Ala193Pro Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala193Val Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala202Val Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala212Val Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala33Pro Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala33Thr Uncertain significance ★★ ⚠ same condition
XRCC2 p.Ala4Ser 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/xrcc2-p-cys2 (accessed [today's date]).

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