cone dystrophy 5, X-linked

disease

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Also known as COD5

Summary

cone dystrophy 5, X-linked (MONDO:0800319) is a disease with 1 cohort gene.

At a glance

Cohort genes: 1
ClinVar variants: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	cone dystrophy 5, X-linked
Mondo ID	MONDO:0800319
UMLS	C3887937
MedGen	854645
Is cancer (heuristic)	no

Also known as: COD5

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › retinal disorder › retinal degeneration › cone dystrophy 5, X-linked

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

1 retrieved; paginated sample, class counts are floors:

1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
10513	NM_000513.2(OPN1MW):c.529T>C (p.Trp177Arg)	OPN1MW	Pathogenic	no assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
OPN1MW	Orphanet:16	Blue cone monochromatism
OPN1MW	Orphanet:1872	Cone rod dystrophy
OPN1MW	Orphanet:90001	X-linked cone dysfunction syndrome with myopia

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
OPN1MW	HGNC:4206	ENSG00000268221	P04001	Medium-wave-sensitive opsin 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
OPN1MW	Medium-wave-sensitive opsin 1	Visual pigments are the light-absorbing molecules that mediate vision.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
GPCR	1	23.9×	0.042

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
OPN1MW	GPCR	yes		GPCR_Rhodpsn, Opsin_red/grn, Opsin

Expression context

Cohort genes with no expression data: 0.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	1
broad (>20)	0
unknown	0

Top tissues across cohort

Tissue	Cohort genes
colonic epithelium	1
male germ line stem cell (sensu Vertebrata) in testis	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
OPN1MW	16		yes	male germ line stem cell (sensu Vertebrata) in testis, colonic epithelium, sural nerve

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
OPN1MW	0

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
OPN1MW	P04001	3

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 4. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways 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.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Defective visual phototransduction due to OPN1MW loss of function	1	11420.0×	4e-04	OPN1MW
The retinoid cycle in cones (daylight vision)	1	1631.4×	0.001	OPN1MW
Opsins	1	1268.9×	0.001	OPN1MW
G alpha (i) signalling events	1	39.0×	0.026	OPN1MW

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
absorption of visible light	1	2808.7×	0.002	OPN1MW
cellular response to light stimulus	1	1053.2×	0.003	OPN1MW
phototransduction	1	495.6×	0.004	OPN1MW
positive regulation of cytokinesis	1	401.2×	0.004	OPN1MW
visual perception	1	79.5×	0.015	OPN1MW
G protein-coupled receptor signaling pathway	1	36.2×	0.028	OPN1MW

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
OPN1MW	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	1	OPN1MW
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

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)
OPN1MW	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: OPN1MW