X-linked cone-rod dystrophy 3

Summary

X-linked cone-rod dystrophy 3 (MONDO:0010335) is a disease caused by CACNA1F (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: CACNA1F (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 35

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	X-linked cone-rod dystrophy 3
Mondo ID	MONDO:0010335
MeSH	C564507
OMIM	300476
DOID	DOID:0111007
UMLS	C1845407
MedGen	336932
GARD	0010654
Is cancer (heuristic)	no

Also known as: cone-rod dystrophy X-linked 3 · cone-rod dystrophy, X-linked, 3 · cone-rod dystrophy, X-linked, 3, X-linked recessive · cone-rod dystrophy, X-linked, type 3 · CORDX3 · X-linked cone-rod dystrophy type 3

Data availability: 35 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › X-linked disease › X-linked cone-rod dystrophy › X-linked cone-rod dystrophy 3

Related subtypes (3): X-linked cone-rod dystrophy 2, blue cone monochromacy, X-linked cone-rod dystrophy 1

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

35 retrieved; paginated sample, class counts are floors:

11 pathogenic, 8 uncertain significance, 5 pathogenic/likely pathogenic, 4 benign/likely benign, 3 likely benign, 2 benign, 2 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1074712	NM_001256789.3(CACNA1F):c.3019G>A (p.Gly1007Arg)	CACNA1F	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
11620	NM_001256789.3(CACNA1F):c.3439-1_3442delinsTGG	CACNA1F	Pathogenic	no assertion criteria provided
1184528	NM_001256789.3(CACNA1F):c.1877+1G>T	CACNA1F	Pathogenic	no assertion criteria provided
1699126	NM_001256789.3(CACNA1F):c.2504del (p.Pro835fs)	CACNA1F	Pathogenic	criteria provided, single submitter
1699338	NM_001256789.3(CACNA1F):c.1855del (p.Leu619fs)	CACNA1F	Pathogenic	criteria provided, single submitter
2026141	NM_001256789.3(CACNA1F):c.3792+2T>C	CACNA1F	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2131362	NM_001256789.3(CACNA1F):c.2086-1G>C	CACNA1F	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
217443	NM_001256789.3(CACNA1F):c.2509G>A (p.Gly837Ser)	CACNA1F	Pathogenic	no assertion criteria provided
217444	NG_009095.2:g.(16929_16947)_(21383_21401)del	CACNA1F	Pathogenic	no assertion criteria provided
2444434	NM_001256789.3(CACNA1F):c.157C>T (p.Gln53Ter)	CACNA1F	Pathogenic	criteria provided, single submitter
265464	NM_001256789.3(CACNA1F):c.1840C>T (p.Arg614Ter)	CACNA1F	Pathogenic	criteria provided, multiple submitters, no conflicts
265465	NM_001256789.3(CACNA1F):c.148C>T (p.Arg50Ter)	CACNA1F	Pathogenic	criteria provided, multiple submitters, no conflicts
285396	NM_001256789.3(CACNA1F):c.2543+1G>A	CACNA1F	Pathogenic	criteria provided, multiple submitters, no conflicts
4721480	NM_001256789.3(CACNA1F):c.1438del (p.Ala480fs)	CACNA1F	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
624415	NM_001256789.3(CACNA1F):c.2086-2A>G	CACNA1F	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
812245	NM_001256789.3(CACNA1F):c.4051C>T (p.Arg1351Ter)	CACNA1F	Pathogenic	criteria provided, multiple submitters, no conflicts
3066214	NM_001256789.3(CACNA1F):c.3591_3595dup (p.Gln1199fs)	CACNA1F	Likely pathogenic	criteria provided, single submitter
369958	NM_001256789.3(CACNA1F):c.3037-2A>G	CACNA1F	Likely pathogenic	no assertion criteria provided
1466612	NM_001256789.3(CACNA1F):c.448G>C (p.Gly150Arg)	CACNA1F	Uncertain significance	criteria provided, multiple submitters, no conflicts
1509434	NM_001256789.3(CACNA1F):c.4862G>C (p.Arg1621Pro)	CACNA1F	Uncertain significance	criteria provided, multiple submitters, no conflicts
2579254	GRCh38/hg38 Xp11.23(chrX:49222435-49226325)x0	CACNA1F	Uncertain significance	criteria provided, single submitter
4072279	NM_001256789.3(CACNA1F):c.1463+6G>A	CACNA1F	Uncertain significance	criteria provided, single submitter
430654	NM_001256789.3(CACNA1F):c.1933A>T (p.Ile645Phe)	CACNA1F	Uncertain significance	no assertion criteria provided
4533390	NM_001256789.3(CACNA1F):c.1255C>A (p.Pro419Thr)	CACNA1F	Uncertain significance	criteria provided, single submitter
587564	NM_001256789.3(CACNA1F):c.1108G>A (p.Val370Ile)	CACNA1F	Uncertain significance	criteria provided, multiple submitters, no conflicts
812250	NM_001256789.3(CACNA1F):c.1276+34G>A	CACNA1F	Uncertain significance	criteria provided, multiple submitters, no conflicts
1192562	NM_001256789.3(CACNA1F):c.3037-30G>A	CACNA1F	Benign	criteria provided, single submitter
1192563	NM_001256789.3(CACNA1F):c.2928+5C>T	CACNA1F	Benign	criteria provided, single submitter
1192564	NM_001256789.3(CACNA1F):c.2334+123G>C	CACNA1F	Benign/Likely benign	criteria provided, multiple submitters, no conflicts
166778	NM_001256789.3(CACNA1F):c.2673+3G>A	CACNA1F	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · 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
CACNA1F	Strong	X-linked	X-linked cone-rod dystrophy 3	7

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
CACNA1F	Orphanet:178333	Åland Islands eye disease
CACNA1F	Orphanet:1872	Cone rod dystrophy
CACNA1F	Orphanet:714070	Incomplete congenital stationary night blindness, Schubert-Bornschein type

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
CACNA1F	HGNC:1393	ENSG00000102001	O60840	Voltage-dependent L-type calcium channel subunit alpha-1F	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CACNA1F	Voltage-dependent L-type calcium channel subunit alpha-1F	Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene exp…

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
Ion channel	1	111.5×	0.009

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CACNA1F	Ion channel	yes		VDCCAlpha1, VDCC_L_a1su, Ion_trans_dom

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
granulocyte	1
parotid gland	1
right hemisphere of cerebellum	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CACNA1F	143	tissue_specific	marker	parotid gland, granulocyte, right hemisphere of cerebellum

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CACNA1F	1,616

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CACNA1F	O60840	67.46

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
negative regulation of voltage-gated calcium channel activity	1	3370.4×	0.001	CACNA1F
detection of light stimulus involved in visual perception	1	648.1×	0.002	CACNA1F
calcium ion import across plasma membrane	1	543.6×	0.002	CACNA1F
visual perception	1	79.5×	0.013	CACNA1F

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 0

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

Symbol	Example approved molecule
CACNA1F	BEPRIDIL

Top cohort targets by molecule count

Symbol	Molecules	Max phase
CACNA1F	48	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
BEPRIDIL	4	CACNA1F
IMIPRAMINE	4	CACNA1F
HALOFANTRINE	4	CACNA1F
DROPERIDOL	4	CACNA1F
SAQUINAVIR	4	CACNA1F
DULOXETINE	4	CACNA1F
DIAZEPAM	4	CACNA1F
SERTINDOLE	4	CACNA1F
QUINIDINE	4	CACNA1F
LAMIVUDINE	4	CACNA1F
PIMOZIDE	4	CACNA1F
PHENYTOIN	4	CACNA1F
TERFENADINE	4	CACNA1F
CISAPRIDE	4	CACNA1F
SOLIFENACIN	4	CACNA1F
NIFEDIPINE	4	CACNA1F
DILTIAZEM	4	CACNA1F
NILOTINIB	4	CACNA1F
ASTEMIZOLE	4	CACNA1F
TERODILINE	4	CACNA1F
CLOZAPINE	4	CACNA1F
MIBEFRADIL	4	CACNA1F
DOFETILIDE	4	CACNA1F
THIORIDAZINE	4	CACNA1F
PAROXETINE	4	CACNA1F
DONEPEZIL	4	CACNA1F
IBUTILIDE	4	CACNA1F
SUNITINIB	4	CACNA1F
HALOPERIDOL	4	CACNA1F
DASATINIB	4	CACNA1F

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
CACNA1F	221	Binding:135, Functional:79, Toxicity:5, ADMET:2

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

Symbol	ChEMBL assays
CACNA1F	221

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

30 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.

Compound	Max phase	Cohort target (bioactivity)
BEPRIDIL	4	CACNA1F
IMIPRAMINE	4	CACNA1F
HALOFANTRINE	4	CACNA1F
DROPERIDOL	4	CACNA1F
SAQUINAVIR	4	CACNA1F
DULOXETINE	4	CACNA1F
DIAZEPAM	4	CACNA1F
SERTINDOLE	4	CACNA1F
QUINIDINE	4	CACNA1F
LAMIVUDINE	4	CACNA1F
PIMOZIDE	4	CACNA1F
PHENYTOIN	4	CACNA1F
TERFENADINE	4	CACNA1F
CISAPRIDE	4	CACNA1F
SOLIFENACIN	4	CACNA1F
NIFEDIPINE	4	CACNA1F
DILTIAZEM	4	CACNA1F
NILOTINIB	4	CACNA1F
ASTEMIZOLE	4	CACNA1F
TERODILINE	4	CACNA1F
CLOZAPINE	4	CACNA1F
MIBEFRADIL	4	CACNA1F
DOFETILIDE	4	CACNA1F
THIORIDAZINE	4	CACNA1F
PAROXETINE	4	CACNA1F
DONEPEZIL	4	CACNA1F
IBUTILIDE	4	CACNA1F
SUNITINIB	4	CACNA1F
HALOPERIDOL	4	CACNA1F
DASATINIB	4	CACNA1F

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	CACNA1F
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	0

Undrugged target profiles

0 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Clinical trials & evidence

Clinical trials

Clinical trials: 0.