Coloboma, ocular, autosomal recessive
diseaseOn this page
Summary
Coloboma, ocular, autosomal recessive (MONDO:0009002) is a disease with 1 cohort gene.
At a glance
- Cohort genes: 1
- ClinVar variants: 4
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | coloboma, ocular, autosomal recessive |
| Mondo ID | MONDO:0009002 |
| OMIM | 216820 |
| UMLS | C4011974 |
| MedGen | 860411 |
| Is cancer (heuristic) | no |
Also known as: coloboma, ocular, autosomal recessive
Data availability: 4 ClinVar variants · 1 GenCC gene-disease record.
Disease family
Classification path: disease › human disease › disease by body system or component › disorder of orbital region › eye disorder › coloboma › coloboma, ocular, autosomal recessive
Related subtypes (7): microphthalmia, isolated, with coloboma, coloboma, ocular, autosomal dominant, coloboma of macula, coloboma of optic nerve, coloboma of eye lens, coloboma of eyelid, calloso-genital dysplasia
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
4 retrieved; paginated sample, class counts are floors:
3 uncertain significance, 1 pathogenic
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 143946 | NM_001364564.1(SALL2):c.79G>T (p.Glu27Ter) | SALL2 | Pathogenic | no assertion criteria provided |
| 1032993 | NM_001364564.1(SALL2):c.662C>T (p.Pro221Leu) | SALL2 | Uncertain significance | criteria provided, single submitter |
| 2435647 | NM_001364564.1(SALL2):c.2286GGA[1] (p.Glu766_Glu767del) | SALL2 | Uncertain significance | criteria provided, single submitter |
| 3780577 | NM_001364564.1(SALL2):c.*634del | SALL2 | Uncertain significance | criteria provided, single submitter |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 1 · Orphanet: 7 · 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 |
|---|---|---|---|---|
| SALL2 | Limited | Unknown | coloboma, ocular, autosomal recessive |
Orphanet rare-disease linkage (cohort genes)
| Gene | Orphanet ID | Rare disease |
|---|---|---|
| SALL2 | Orphanet:98942 | Coloboma of choroid and retina |
| SALL2 | Orphanet:98943 | Coloboma of eye lens |
| SALL2 | Orphanet:98944 | Coloboma of iris |
| SALL2 | Orphanet:98945 | Coloboma of macula |
| SALL2 | Orphanet:98946 | Coloboma of eyelid |
| SALL2 | Orphanet:98947 | Coloboma of optic disc |
| SALL2 | Orphanet:99861 | Precursor T-cell acute lymphoblastic leukemia |
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 |
|---|---|---|---|---|---|
| SALL2 | HGNC:10526 | ENSG00000165821 | Q9Y467 | Sal-like protein 2 | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| SALL2 | Sal-like protein 2 | Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure. |
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) |
|---|---|---|---|---|
| SALL2 | Transcription factor | no | Znf_C2H2_type, Znf_C2H2_sf, Sal_C2H2-zinc-finger |
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 |
|---|---|
| cerebellar vermis | 1 |
| paraflocculus | 1 |
| superior vestibular nucleus | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| SALL2 | 243 | ubiquitous | marker | cerebellar vermis, superior vestibular nucleus, paraflocculus |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| SALL2 | 1,277 |
Structural data
PDB: 0 · AlphaFold-only: 1 · No structure: 0
AlphaFold-only cohort genes (top 30 by pLDDT)
| Symbol | UniProt | pLDDT |
|---|---|---|
| SALL2 | Q9Y467 | 52.09 |
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 |
|---|---|---|---|---|
| eye development | 1 | 351.1× | 0.009 | SALL2 |
| positive regulation of transcription by RNA polymerase II | 1 | 14.9× | 0.086 | SALL2 |
| regulation of transcription by RNA polymerase II | 1 | 11.7× | 0.086 | SALL2 |
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 |
|---|---|---|
| SALL2 | 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 | SALL2 |
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) |
|---|---|---|
| SALL2 | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: SALL2