Is STAG2 p.Ile30= (c.90C>T) pathogenic?

STAG2 p.Ile30= (c.90C>T) is classified Likely benign in STAG2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-15). Very rare (popmax 0.00308%, eas).

How common is STAG2 p.Ile30= (c.90C>T) in the general population?

STAG2 p.Ile30= (c.90C>T) is very rare (popmax 0.00308%, eas) (gnomAD).

STAG2 p.Ile30=

c.90C>T · rs1255264404 · VCV1670622

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00308%, eas)

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 -0.2	GERP -3.5, phastCons 0.59
Overall
CADD	5.392	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00308% East Asian · 1/32,461 alleles

Filtering AF 9.1e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.5e-05%

Overall 0.000506% 6/1,185,978 alleles · very rare exomes 6/1,073,840 · genomes 0/112,138 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00308%	32,461
Finnishnot grpmax-eligible	0.00218%	45,878
Remaining individualsnot grpmax-eligible	0.00215%	46,588
European (non-Finnish)	0.00034%	293,911

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: STAG2
Protein: p.Ile30=
Coding: c.90C>T
MANE Select: NM_001042750
dbSNP: rs1255264404
Type: single nucleotide variant
Location: chrX:124025885 (GRCh38)
Structure: AlphaFold pLDDT 80.07 · 10 PDB
Residue 30: the 'disordered' region

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

Similar variants

STAG2 p.Ile30Val Uncertain significance ★ ⚠ same residue
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

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-ile30 (accessed [today's date]).

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