Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome: genes and variants
Explore variant evidence for Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome across 1 analyzed protein (COMP). Linked ClinVar records include 32 pathogenic or likely pathogenic variants, 16 variants of uncertain significance and 11 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 Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome
COMP: Cartilage oligomeric matrix protein
An extracellular-matrix protein that interacts with collagens and other cartilage components to support cartilage structure. Variants can cause pseudoachondroplasia or multiple epiphyseal dysplasia.
32 ClinVar pathogenic / likely pathogenic and 27 uncertain variants in COMP have source records linked to Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome. Association strength is not clinical gene validity.
Where Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome variants cluster
- COMP TSP type-3 1 (positions 268–300): 6 of 32 ClinVar pathogenic / likely pathogenic variants, 4.3× more than its size predicts.
- COMP TSP type-3 7 (positions 457–492): 6 of 32 ClinVar pathogenic / likely pathogenic variants, 3.9× more than its size predicts.
- COMP TSP type-3 8 (positions 493–528): 4 of 32 ClinVar pathogenic / likely pathogenic variants, 2.6× more than its size predicts.
- COMP TSP type-3 5 (positions 396–418): 3 of 32 ClinVar pathogenic / likely pathogenic variants, 3.1× more than its size predicts.
- COMP TSP type-3 6 (positions 419–456): 4 of 32 ClinVar pathogenic / likely pathogenic variants, 2.5× more than its size predicts.
ClinVar pathogenic and likely pathogenic variants linked to Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| COMP D273V | 273 | TSP type-3 1 | Pathogenic / likely pathogenic (★★★★) |
| COMP D437N | 437 | TSP type-3 6 | Pathogenic / likely pathogenic (★★) |
| COMP D439G | 439 | TSP type-3 6 | Pathogenic / likely pathogenic (★★) |
| COMP D439Y | 439 | TSP type-3 6 | Pathogenic / likely pathogenic (★★) |
| COMP D518H | 518 | TSP type-3 8 | Pathogenic / likely pathogenic (★★) |
| COMP D518N | 518 | TSP type-3 8 | Pathogenic / likely pathogenic (★★) |
| COMP D269G | 269 | TSP type-3 1 | Pathogenic / likely pathogenic (★★) |
| COMP C292R | 292 | TSP type-3 1 | Pathogenic / likely pathogenic (★★) |
| COMP G299R | 299 | TSP type-3 1 | Pathogenic / likely pathogenic (★★) |
| COMP G309R | 309 | TSP type-3 2 | Pathogenic / likely pathogenic (★★) |
| COMP D349H | 349 | TSP type-3 3 | Pathogenic / likely pathogenic (★★) |
| COMP D385N | 385 | TSP type-3 4 | Pathogenic / likely pathogenic (★★) |
| COMP D399N | 399 | TSP type-3 5 | Pathogenic / likely pathogenic (★★) |
| COMP C468F | 468 | TSP type-3 7 | Pathogenic / likely pathogenic (★★) |
| COMP G719D | 719 | TSP C-terminal | Pathogenic / likely pathogenic (★★) |
| COMP D437H | 437 | TSP type-3 6 | Pathogenic / likely pathogenic (★) |
| COMP D473H | 473 | TSP type-3 7 | Pathogenic / likely pathogenic (★) |
| COMP C328F | 328 | TSP type-3 2 | Pathogenic / likely pathogenic (★) |
| COMP D401H | 401 | TSP type-3 5 | Pathogenic / likely pathogenic (★) |
| COMP D515E | 515 | TSP type-3 8 | Pathogenic / likely pathogenic (★) |
| COMP N297K | 297 | TSP type-3 1 | Pathogenic / likely pathogenic (★) |
| COMP C351R | 351 | TSP type-3 3 | Pathogenic / likely pathogenic (★) |
| COMP D376Y | 376 | TSP type-3 4 | Pathogenic / likely pathogenic (★) |
| COMP G465V | 465 | TSP type-3 7 | Pathogenic / likely pathogenic (★) |
| COMP D482V | 482 | TSP type-3 7 | Pathogenic / likely pathogenic (★) |
| COMP D507E | 507 | TSP type-3 8 | Pathogenic / likely pathogenic (★) |
| COMP T585R | 585 | TSP C-terminal | Pathogenic / likely pathogenic (★) |
| COMP D473G | 473 | TSP type-3 7 | Pathogenic / likely pathogenic |
| COMP C328R | 328 | TSP type-3 2 | Pathogenic / likely pathogenic |
| COMP D472Y | 472 | TSP type-3 7 | Pathogenic / likely pathogenic |
| COMP D290Y | 290 | TSP type-3 1 | Pathogenic / likely pathogenic |
| COMP G404R | 404 | TSP type-3 5 | Pathogenic / likely pathogenic |
Uncertain variants prioritized for review in Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome
| Variant | Position | Protein part | Clinical label | Evidence |
|---|---|---|---|---|
| COMP D437Y | 437 | TSP type-3 6 | Conflicting reports (★) | +6: 4 other pathogenic changes within 3 positions; D437H at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.97 |
| COMP D290G | 290 | TSP type-3 1 | Conflicting reports (★) | +6: 2 other pathogenic changes within 3 positions; D290Y at the same position is pathogenic; not seen in the gnomAD population database; AlphaMissense 0.99 |
Which prediction tools work for Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome
Observed separation of ClinVar pathogenic / likely pathogenic from benign / likely benign variants (AUROC × 100). This benchmark is not a clinical recommendation.
- CATVariant: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
- ESM1b (LLR): 94 out of 100
- AlphaMissense: 92 out of 100
- SIFT: 79 out of 100
- PolyPhen-2: 69 out of 100 (learned from overlapping clinical labels, so this is optimistic)
Same protein, different disease
- Multiple epiphyseal dysplasia also has ClinVar records linked to COMP variants; they fall partly in the same places as the Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome variants (27 pathogenic / likely pathogenic).
Diseases related to Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome
- Multiple epiphyseal dysplasia, also linked to COMP
- Connective tissue disease, also linked to COMP
- Carpal tunnel syndrome, also linked to COMP
Frequently asked questions
Which genes have records linked to Pseudoachondroplastic spondyloepiphyseal dysplasia syndrome?
This view contains 1 analyzed proteins: COMP. 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 32 pathogenic or likely pathogenic variants, 16 variants of uncertain significance and 11 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 61 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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