Leber congenital amaurosis 7
disease diseaseOn this page
Also known as CRX Leber congenital amaurosisLCA7Leber congenital amaurosis caused by mutation in CRXLeber congenital amaurosis type 7
Summary
Leber congenital amaurosis 7 (MONDO:0013449) is a disease caused by CRX (GenCC Definitive), with 1 cohort gene.
At a glance
- Causal gene: CRX (GenCC Definitive)
- Cohort genes: 1
- ClinVar variants: 473
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | Leber congenital amaurosis 7 |
| Mondo ID | MONDO:0013449 |
| OMIM | 613829 |
| DOID | DOID:0110333 |
| UMLS | C3151192 |
| MedGen | 462542 |
| GARD | 0010880 |
| Is cancer (heuristic) | no |
Also known as: CRX Leber congenital amaurosis · LCA7 · Leber congenital amaurosis 7 · Leber congenital amaurosis caused by mutation in CRX · Leber congenital amaurosis type 7
Data availability: 473 ClinVar variants · 5 GenCC gene-disease records.
Disease family
Classification path: disease › human disease › disease by body system or component › nervous system disorder › congenital nervous system disorder › Leber congenital amaurosis › Leber congenital amaurosis 7
Related subtypes (20): retinal aplasia, Leber congenital amaurosis 1, Leber congenital amaurosis 2, Leber congenital amaurosis 3, Leber congenital amaurosis 4, Leber congenital amaurosis 5, Leber congenital amaurosis 9, Leber congenital amaurosis 12, Leber congenital amaurosis 10, Leber congenital amaurosis 13, Leber congenital amaurosis 14, Leber congenital amaurosis 6, Leber congenital amaurosis 8, Leber congenital amaurosis 11, Leber congenital amaurosis 15, Leber congenital amaurosis 16, Leber congenital amaurosis 17, Leber congenital amaurosis 19, Leber congenital amaurosis with early-onset deafness, Leber congenital amaurosis 18
Genetics & variants
GWAS landscape
No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.
Variant details and genetic-evidence tiers
ClinVar germline variants
473 retrieved; paginated sample, class counts are floors:
188 uncertain significance, 81 pathogenic, 81 likely benign, 37 conflicting classifications of pathogenicity, 33 benign, 24 benign/likely benign, 18 pathogenic/likely pathogenic, 11 likely pathogenic
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 1004054 | NM_000554.6(CRX):c.728dup (p.Pro244fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1013687 | NM_000554.6(CRX):c.660dup (p.Tyr221fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1020865 | NM_000554.6(CRX):c.263A>G (p.Lys88Arg) | CRX | Pathogenic/Likely pathogenic | criteria provided, multiple submitters, no conflicts |
| 1035273 | NM_000554.6(CRX):c.323del (p.Pro108fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1037927 | NM_000554.6(CRX):c.426C>A (p.Tyr142Ter) | CRX | Pathogenic | criteria provided, single submitter |
| 1043624 | NM_000554.6(CRX):c.592del (p.Ala198fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1046426 | NC_000019.9:g.(?48337701)(48343224_?)del | CRX | Pathogenic | criteria provided, single submitter |
| 1056395 | NM_000554.6(CRX):c.76_80del (p.Met26fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1071706 | NC_000019.9:g.(?48339500)(48343224_?)del | CRX | Pathogenic | criteria provided, single submitter |
| 1172711 | NM_000554.6(CRX):c.564del (p.Ala189fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1184468 | NM_000554.6(CRX):c.522_523dup (p.Gln175fs) | CRX | Pathogenic | no assertion criteria provided |
| 1359713 | NM_000554.6(CRX):c.509del (p.Pro170fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1370793 | NM_000554.6(CRX):c.324del (p.Gly110fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1385024 | NM_000554.6(CRX):c.381del (p.Ser128fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1387234 | NM_000554.6(CRX):c.125_128dup (p.Thr44fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1393381 | NM_000554.6(CRX):c.365del (p.Gly122fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1399832 | NM_000554.6(CRX):c.590del (p.Pro197fs) | CRX | Pathogenic | criteria provided, multiple submitters, no conflicts |
| 1418367 | NM_000554.6(CRX):c.750del (p.Thr251fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1425620 | NM_000554.6(CRX):c.176_177del (p.Ala59fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1466734 | NM_000554.6(CRX):c.501del (p.Glu168fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1468996 | NM_000554.6(CRX):c.108del (p.Arg37fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1478978 | NM_000554.6(CRX):c.494del (p.Pro165fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1496447 | NM_000554.6(CRX):c.624T>G (p.Tyr208Ter) | CRX | Pathogenic | criteria provided, single submitter |
| 1499937 | NM_000554.6(CRX):c.597del (p.Ala200fs) | CRX | Pathogenic | criteria provided, single submitter |
| 1685674 | NM_000554.6(CRX):c.545C>G (p.Ser182Ter) | CRX | Pathogenic | criteria provided, multiple submitters, no conflicts |
| 2007366 | NM_000554.6(CRX):c.541_542del (p.Ala181fs) | CRX | Pathogenic | criteria provided, single submitter |
| 2014678 | NM_000554.6(CRX):c.116_127del (p.Gln39_Glu42del) | CRX | Pathogenic | criteria provided, single submitter |
| 2017828 | NM_000554.6(CRX):c.591_594dup (p.Ser199fs) | CRX | Pathogenic | criteria provided, single submitter |
| 2033764 | NM_000554.6(CRX):c.714del (p.Gly239fs) | CRX | Pathogenic | criteria provided, single submitter |
| 2071819 | NM_000554.6(CRX):c.557del (p.Leu186fs) | CRX | Pathogenic | criteria provided, single submitter |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 10 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0
GenCC gene–disease validity (cohort genes)
the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.
| Gene | Classification | Inheritance | Disease | Records |
|---|---|---|---|---|
| CRX | Definitive | Semidominant | Leber congenital amaurosis 7 | 10 |
Orphanet rare-disease linkage (cohort genes)
| Gene | Orphanet ID | Rare disease |
|---|---|---|
| CRX | Orphanet:1872 | Cone rod dystrophy |
| CRX | Orphanet:65 | Leber congenital amaurosis |
| CRX | Orphanet:791 | Retinitis pigmentosa |
Cohort genes → proteins
1 cohort genes, 1 distinct canonical proteins.
Evidence partition
| Subset | Genes |
|---|---|
| multi_evidence | 1 |
Cohort genes (full)
| Symbol | HGNC | Ensembl | UniProt | Name | Evidence |
|---|---|---|---|---|---|
| CRX | HGNC:2383 | ENSG00000105392 | O43186 | Cone-rod homeobox protein | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| CRX | Cone-rod homeobox protein | Transcription factor that binds and transactivates the sequence 5’-TAATC[CA]-3’ which is found upstream of several photoreceptor-specific genes, including the opsin genes. |
Protein-family classification
Druggable: 0 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.0
Family distribution
Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.
| Family | Genes | Fold | FDR |
|---|---|---|---|
| Transcription factor | 1 | 8.3× | 0.121 |
Per-gene assignment
| Symbol | Family | Druggable? | EC | InterPro (top 3) |
|---|---|---|---|---|
| CRX | Transcription factor | no | HD, Homeodomain-like_sf, Otx_TF_C |
Expression context
Cohort genes with no expression data: 0.
1 cohort gene are a single-cell marker in ≥1 SCXA experiment.
Breadth distribution (Bgee present_calls)
| Bucket | Genes |
|---|---|
| narrow (1-5 tissues) | 0 |
| moderate (6-20) | 0 |
| broad (>20) | 1 |
| unknown | 0 |
Top tissues across cohort
| Tissue | Cohort genes |
|---|---|
| pigmented layer of retina | 1 |
| primordial germ cell in gonad | 1 |
| retina | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| CRX | 54 | tissue_specific | marker | pigmented layer of retina, retina, primordial germ cell in gonad |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| CRX | 2,076 |
Structural data
PDB: 1 · AlphaFold-only: 0 · No structure: 0
Cohort genes with PDB structures (top 30)
| Symbol | UniProt | PDB entries |
|---|---|---|
| CRX | O43186 | 1 |
Function
Pathway analysis
Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).
GO biological processes by enrichment
Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| GO term | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| retina development in camera-type eye | 1 | 255.3× | 0.021 | CRX |
| animal organ morphogenesis | 1 | 191.5× | 0.021 | CRX |
| visual perception | 1 | 79.5× | 0.034 | CRX |
| nervous system development | 1 | 45.9× | 0.044 | CRX |
| regulation of DNA-templated transcription | 1 | 31.6× | 0.046 | CRX |
| cell differentiation | 1 | 29.1× | 0.046 | CRX |
| positive regulation of transcription by RNA polymerase II | 1 | 14.9× | 0.077 | CRX |
| regulation of transcription by RNA polymerase II | 1 | 11.7× | 0.086 | CRX |
Therapeutics
Drug target analysis
Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1
Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).
Top cohort targets by molecule count
| Symbol | Molecules | Max phase |
|---|---|---|
| CRX | 0 | 0 |
Bioactivity and enzyme data
Enzyme cohort genes (≥1 EC): 0.
Pharmacogenomics
Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.
No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).
Chemical tractability of cohort targets
0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.
Druggability pyramid
Cohort genes binned by druggability tier (high → low):
| Tier | Definition | Genes | Symbols |
|---|---|---|---|
| A | Approved (phase 4 drug) | 0 | |
| B | Phased (≥1) drug, not yet approved | 0 | |
| C | Druggable family + PDB, no drug | 0 | |
| D | Druggable family + AlphaFold only, no drug | 0 | |
| E | Difficult family or no structure, no drug | 1 | CRX |
Undrugged target profiles
1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).
| Symbol | ChEMBL assays | Drugged partners (top 3) |
|---|---|---|
| CRX | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: CRX