Is STAG2 p.Pro1237= (c.3711A>C) pathogenic?

STAG2 p.Pro1237= (c.3711A>C) is classified Likely benign in STAG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-25). Absent from gnomAD v4.1.

How common is STAG2 p.Pro1237= (c.3711A>C) in the general population?

STAG2 p.Pro1237= (c.3711A>C) is absent from gnomAD v4.1 (gnomAD).

STAG2 p.Pro1237=

c.3711A>C · rs2522558292 · VCV2982133

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 1.5	GERP -5, phastCons 1
Overall
CADD	7.683	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: STAG2
Protein: p.Pro1237=
Coding: c.3711A>C
MANE Select: NM_001042750
dbSNP: rs2522558292
Type: single nucleotide variant
Location: chrX:124095377 (GRCh38)
Structure: AlphaFold pLDDT 80.07 · 10 PDB

Full STAG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

STAG2 p.Arg1012Ter Pathogenic ★★ same type
STAG2 p.Arg1033Ter Pathogenic ★★ same type
STAG2 c.1018-3T>A Uncertain significance ★★ same type
STAG2 c.2924+3A>G Uncertain significance ★★ same type
STAG2 c.2924+5T>A Uncertain significance ★★ same type
STAG2 c.3784-3T>C Uncertain significance ★★ same type
STAG2 p.Ala428Gly Uncertain significance ★★ ⚠ same type
STAG2 p.Ala532Val Uncertain significance ★★ ⚠ same type

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/stag2-p-pro1237 (accessed [today's date]).

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