Chromosome 2q32-q33 deletion syndrome: genes and variants
Explore variant evidence for Chromosome 2q32-q33 deletion syndrome across 1 analyzed protein (SATB2). Linked ClinVar records include 22 pathogenic or likely pathogenic variants, 126 variants of uncertain significance and 28 with conflicting classifications.
Coverage includes proteins already analyzed in CATVariant, not every gene involved in this condition. Database links are associations, not an assessment of clinical gene–disease validity. Computable evidence prioritizes variants for expert review and does not reclassify them. Counts refer to the selected disease label.
Data updated 2026-10-11. Automated aggregation, not a clinical review date.
Download variant evidence (CSV)
Genes linked to Chromosome 2q32-q33 deletion syndrome
SATB2: DNA-binding protein SATB2
A DNA-binding chromatin organizer that regulates developmental gene expression. Variants can cause a syndrome affecting speech, cognition, teeth, and palate development.
22 ClinVar pathogenic / likely pathogenic and 154 uncertain variants in SATB2 have source records linked to Chromosome 2q32-q33 deletion syndrome. Association strength is not clinical gene validity.
Where Chromosome 2q32-q33 deletion syndrome variants cluster
- SATB2 CUT 1 (positions 350–437): 12 of 22 ClinVar pathogenic / likely pathogenic variants, 4.5× more than its size predicts.
- SATB2 CUT 2 (positions 473–560): 4 of 22 ClinVar pathogenic / likely pathogenic variants, 1.5× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Chromosome 2q32-q33 deletion syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| SATB2 R399C | 399 | CUT 1 | Pathogenic / likely pathogenic (★★★★) |
| SATB2 R399H | 399 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 R389L | 389 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 G392R | 392 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 E402K | 402 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 Q409R | 409 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 G515D | 515 | CUT 2 | Pathogenic / likely pathogenic (★★) |
| SATB2 R429Q | 429 | CUT 1 | Pathogenic / likely pathogenic (★★) |
| SATB2 S649L | 649 | Homeobox | Pathogenic / likely pathogenic (★★) |
| SATB2 G116R | 116 | CMP | Pathogenic / likely pathogenic (★★) |
| SATB2 E566K | 566 | Pathogenic / likely pathogenic (★★) | |
| SATB2 R522C | 522 | CUT 2 | Pathogenic / likely pathogenic (★★) |
| SATB2 T390I | 390 | CUT 1 | Pathogenic / likely pathogenic (★) |
| SATB2 Q391P | 391 | CUT 1 | Pathogenic / likely pathogenic (★) |
| SATB2 E396G | 396 | CUT 1 | Pathogenic / likely pathogenic (★) |
| SATB2 Y433S | 433 | CUT 1 | Pathogenic / likely pathogenic (★) |
| SATB2 F222S | 222 | CUTL | Pathogenic / likely pathogenic (★) |
| SATB2 E436V | 436 | CUT 1 | Pathogenic / likely pathogenic (★) |
| SATB2 E519K | 519 | CUT 2 | Pathogenic / likely pathogenic (★) |
| SATB2 N665S | 665 | Homeobox | Pathogenic / likely pathogenic (★) |
| SATB2 R88W | 88 | CMP | Pathogenic / likely pathogenic (★) |
| SATB2 G515S | 515 | CUT 2 | Pathogenic / likely pathogenic |
Uncertain variants prioritized for review in Chromosome 2q32-q33 deletion syndrome
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| SATB2 R389H | 389 | CUT 1 | Conflicting reports (★) | +6: 4 other pathogenic changes within 3 positions; R389L at the same position is pathogenic; seen in 7e-07 of gnomAD DNA copies; REVEL 0.679 |
| SATB2 R399P | 399 | CUT 1 | Conflicting reports (★) | +6: 4 other pathogenic changes within 3 positions; R399C at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 1.00 |
Which prediction tools work for Chromosome 2q32-q33 deletion syndrome
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- AlphaMissense: 99 out of 100
- ESM1b (LLR): 96 out of 100
- PolyPhen-2: 95 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- MutPred2: 94 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- CATVariant: 93 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- SIFT: 88 out of 100
- EVE: 88 out of 100
- MetaLR: 81 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- DMS / MaveDB: 56 out of 100
Diseases related to Chromosome 2q32-q33 deletion syndrome
- Developmental disorder, also linked to SATB2
Frequently asked questions
Which genes have records linked to Chromosome 2q32-q33 deletion syndrome?
This view contains 1 analyzed proteins: SATB2. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.
What do the clinical classifications mean?
Linked records include 22 pathogenic or likely pathogenic variants, 126 variants of uncertain significance and 28 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.
Does the evidence score change a VUS classification?
No. 2 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.
Can I download the variant evidence?
Download the CSV for all 271 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.
About this data
Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.
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