STAG3

Chr 7AR

STAG3 cohesin complex component

Also known as: SA3, SPGF61

The protein is a meiosis-specific component of the cohesin complex that maintains sister chromatid cohesion during cell division by forming a proteinaceous ring that traps sister chromatids until anaphase. Mutations cause premature ovarian failure and male spermatogenic failure, reflecting the protein's essential role in meiotic chromosome segregation in germ cells. The condition follows autosomal recessive inheritance and primarily affects reproductive function.

OMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismARLOEUF 0.612 OMIM phenotypes
Clinical SummarySTAG3
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
0.61LOEUF
pLI 0.000
Z-score 4.32
OE 0.45 (0.340.61)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.66Z-score
OE missense 0.82 (0.770.88)
569 obs / 691.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.45 (0.340.61)
00.351.4
Missense OE0.82 (0.770.88)
00.61.4
Synonymous OE0.92
01.21.6
LoF obs/exp: 33 / 72.8Missense obs/exp: 569 / 691.7Syn Z: 1.08
DN
0.6646th %ile
GOF
0.5464th %ile
LOF
0.2969th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

STAG3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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