Is STAG2 p.Ser853= (c.2559T>C) pathogenic?

STAG2 p.Ser853= (c.2559T>C) is classified Benign/Likely benign in STAG2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-02-26). Very rare (popmax 0.00224%, nfe).

How common is STAG2 p.Ser853= (c.2559T>C) in the general population?

STAG2 p.Ser853= (c.2559T>C) is very rare (popmax 0.00224%, nfe) (gnomAD).

STAG2 p.Ser853=

c.2559T>C · rs752791141 · VCV1586884

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00224%, nfe)

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 2.3	GERP 0.84, phastCons 1
Overall
CADD	9.206	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% European (non-Finnish) · 20/894,285 alleles

Filtering AF 0.00146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00119%

Overall 0.00174% 21/1,208,422 alleles · very rare exomes 17/1,096,157 · genomes 4/112,265 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00224%	44,714
Remaining individualsnot grpmax-eligible	0.0021%	47,524

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.Ser853=
Coding: c.2559T>C
MANE Select: NM_001042750
dbSNP: rs752791141
Type: single nucleotide variant
Location: chrX:124076357 (GRCh38)
Structure: AlphaFold pLDDT 80.07 · 10 PDB
Residue 853: an α-helix; a UniProt-annotated variant site (in hpe13 and mkms; patient cells show decreased protein abundance; increased sister chromatid cohesion); a UniProt-annotated variant site (in mkms); a UniProt-annotated variant site (in hpe13)

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-ser853 (accessed [today's date]).

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