Condition-associated pathogenic-record facets
This page groups public ClinVar pathogenic/likely pathogenic records by ClinVar condition annotation and connects supported groups to transcript-unit coverage and architecture summaries. Here, “recovered” means that transcript-unit coverage was available for the gene-condition group under the current all-mapped release index. Groups outside the covered index are retained as record groups but are not assigned unit-level coverage in this release.
How to use condition facets
Condition facets group ClinVar pathogenic/likely pathogenic records by gene and ClinVar condition annotation, then connect supported groups to transcript-unit coverage and architecture summaries.
1. Record support
Start with the gene-condition record count. Sparse groups should be read cautiously.
2. Architecture class
Read whether the condition group is local, boundary-CDS-associated, donor/payload-burdened, or mechanism-complex.
3. Unit coverage
Use condition-unit rows to see which transcript units cover the condition-associated records.
4. Payload/context caveat
Interpret high record-level coverage together with payload size, boundary context, and mechanism caveats.
In this page, “recovered” means that transcript-unit coverage was recovered for a supported condition-associated record group in the current all-mapped release.
Recovered condition-facet scale
| High-support condition groups | 3,389 |
|---|---|
| High-support groups with recovered unit coverage | 1,278 |
| Global recovered fraction | 37.7% |
| Covered-index gene-universe high-support groups | 1,278 |
| Covered-index groups with unit coverage | 1,278 |
| Covered-index recovery fraction | 100.0% |
| Condition-unit coverage rows | 160,125 |
Condition architecture classes
| Class | Gene-condition groups | Interpretation |
|---|---|---|
| Record-support-limited group | 28,884 | Sparse support; do not overinterpret condition-level architecture. |
| High-support group without recovered unit coverage | 2,110 | Group retained, but no matched transcript-unit coverage is assigned in the current release. |
| Boundary-CDS coverage architecture | 871 | Boundary-driven CDS coverage; interpret with payload and transcript-context caveats. |
| Tumor-predisposition control context | 239 | Caution/control context, not replacement suitability. |
| Local compact architecture | 88 | Condition-associated records concentrate in a local exon/block pattern. |
| Diffuse/moderate architecture | 27 | No compact unit dominates the condition-associated record burden. |
| Boundary-CDS coverage with large-payload burden | 21 | High coverage depends on a larger coding-payload context. |
| Donor/payload-burden caveat | 19 | Apparent coverage depends on donor span or payload burden. |
| Mechanism-complex limitation | 14 | Mechanism-specific biology limits transcript-unit interpretation. |
Representative condition-facet examples
| Gene | Condition label | Class | Records | Best local coverage | Best boundary-CDS coverage |
|---|---|---|---|---|---|
| GLA | Fabry disease | Local compact architecture | 1,089 | 0.724518 | 0.841139 |
| ACVRL1 | Telangiectasia, hereditary hemorrhagic, type 2 | Local compact architecture | 444 | 0.673423 | 0.997748 |
| SMPD1 | Niemann-Pick disease, type A | Local compact architecture | 367 | 0.869210 | 0.869210 |
| ARSA | Metachromatic leukodystrophy | Local compact architecture | 346 | 0.725434 | 0.907514 |
| IDUA | Mucopolysaccharidosis type 1 | Local compact architecture | 334 | 0.508982 | 0.919162 |
| GCDH | Glutaric aciduria, type 1 | Local compact architecture | 322 | 0.602484 | 0.993789 |
| FBN1 | Marfan syndrome | Boundary-CDS coverage architecture | 2,904 | 0.098485 | 0.998623 |
| FBN1 | Familial thoracic aortic aneurysm and aortic dissection | Boundary-CDS coverage architecture | 2,364 | 0.102792 | 0.999154 |
| PKD1 | Polycystic kidney disease, adult type | Boundary-CDS coverage architecture | 1,616 | 0.311881 | 0.974629 |
| DMD | Duchenne muscular dystrophy | Boundary-CDS coverage architecture | 1,600 | 0.098125 | 0.986250 |
| LDLR | Hypercholesterolemia, familial, 1 | Boundary-CDS coverage architecture | 1,532 | 0.434726 | 0.964752 |
| CFTR | Cystic fibrosis | Boundary-CDS coverage architecture | 1,288 | 0.290373 | 0.951087 |
| TTN | Dilated cardiomyopathy 1G | Boundary-CDS coverage with large-payload burden | 4,510 | 0.227716 | 0.996009 |
| TTN | Autosomal recessive limb-girdle muscular dystrophy type 2J | Boundary-CDS coverage with large-payload burden | 4,105 | 0.223630 | 0.995859 |
| NEB | Nemaline myopathy 2 | Boundary-CDS coverage with large-payload burden | 1,554 | 0.065637 | 0.996782 |
| TTN | Cardiovascular phenotype | Boundary-CDS coverage with large-payload burden | 1,167 | 0.272494 | 0.998286 |
| NEB | Arthrogryposis multiplex congenita 6 | Boundary-CDS coverage with large-payload burden | 581 | 0.091222 | 0.998279 |
| SYNE1 | Autosomal recessive ataxia, Beauce type | Boundary-CDS coverage with large-payload burden | 235 | 0.097872 | 0.995745 |
| EXT1 | Multiple congenital exostosis | Donor/payload-burden caveat | 424 | 0.679245 | 0.580189 |
| PCDH19 | Developmental and epileptic encephalopathy, 9 | Donor/payload-burden caveat | 344 | 0.970930 | 0.168605 |
| AR | Androgen resistance syndrome | Donor/payload-burden caveat | 270 | 0.725926 | 0.696296 |
| ARSB | Mucopolysaccharidosis type 6 | Donor/payload-burden caveat | 251 | 0.760956 | 0.717131 |
| PRPH2 | PRPH2-related disorder | Donor/payload-burden caveat | 240 | 0.995833 | 0.575000 |
| TYR | Oculocutaneous albinism type 1A | Donor/payload-burden caveat | 161 | 1.000000 | 0.503106 |
| NF1 | Neurofibromatosis, type 1 | Tumor-predisposition control context | 4,600 | 0.155217 | 0.980870 |
| BRCA2 | Breast-ovarian cancer, familial, susceptibility to, 2 | Tumor-predisposition control context | 3,395 | 0.641532 | 0.995582 |
| BRCA2 | Hereditary breast ovarian cancer syndrome | Tumor-predisposition control context | 3,209 | 0.638205 | 0.992521 |
| BRCA1 | Breast-ovarian cancer, familial, susceptibility to, 1 | Tumor-predisposition control context | 2,883 | 0.661117 | 0.984738 |
| BRCA2 | Hereditary cancer-predisposing syndrome | Tumor-predisposition control context | 2,743 | 0.638352 | 0.996719 |
| ATM | Ataxia-telangiectasia syndrome | Tumor-predisposition control context | 2,437 | 0.121461 | 0.991383 |
| RMRP | Anauxetic dysplasia | Mechanism-complex limitation | 233 | 0.845494 | — |
| RMRP | Metaphyseal chondrodysplasia, McKusick type | Mechanism-complex limitation | 186 | 0.876344 | — |
| HBA2 | alpha Thalassemia | Mechanism-complex limitation | 157 | 0.955414 | 0.700637 |
| HBA1 | alpha Thalassemia | Mechanism-complex limitation | 118 | 0.915254 | 0.618644 |
| HBA1 | Erythrocytosis, familial, 7 | Mechanism-complex limitation | 35 | 0.942857 | 0.628571 |
| RMRP | Metaphyseal dysplasia without hypotrichosis | Mechanism-complex limitation | 29 | 0.931034 | — |
| ABCD1 | Adrenoleukodystrophy | Diffuse/moderate architecture | 444 | 0.632883 | 0.590090 |
| LMNA | Charcot-Marie-Tooth disease type 2 | Diffuse/moderate architecture | 354 | 0.579096 | 0.728814 |
| NAGLU | Mucopolysaccharidosis, MPS-III-B | Diffuse/moderate architecture | 278 | 0.766187 | 0.766187 |
| SLC22A5 | Renal carnitine transport defect | Diffuse/moderate architecture | 274 | 0.667883 | 0.722628 |
| EDA | Hypohidrotic X-linked ectodermal dysplasia | Diffuse/moderate architecture | 243 | 0.674897 | 0.794239 |
| HNF1A | Monogenic diabetes | Diffuse/moderate architecture | 230 | 0.860870 | 0.782609 |
Downloads
- gene_condition_record_groups_v1.tsv
- gene_condition_record_architecture_recovered_v1.tsv
- gene_condition_unit_coverage_recovered_v1.tsv
- condition_architecture_class_summary_recovered_v1.tsv
- condition_facet_representative_examples_v1.tsv
Release links
Browser: https://best916116-crypto.github.io/PrimeReplace-Atlas/
Repository: https://github.com/best916116-crypto/PrimeReplace-Atlas
Zenodo archive: https://doi.org/10.5281/zenodo.20338345