Cone-rod dystrophy 5
disease diseaseOn this page
Also known as cone-rod dystrophy caused by mutation in PITPNM3cone-rod dystrophy type 5CORD5PITPNM3 cone-rod dystrophy
Summary
Cone-rod dystrophy 5 (MONDO:0010969) is a disease caused by PITPNM3 (GenCC Strong), with 1 cohort gene.
At a glance
- Causal gene: PITPNM3 (GenCC Strong)
- Cohort genes: 1
- ClinVar variants: 162
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | cone-rod dystrophy 5 |
| Mondo ID | MONDO:0010969 |
| MeSH | C563415 |
| OMIM | 600977 |
| DOID | DOID:0111010 |
| UMLS | C1832976 |
| MedGen | 322083 |
| GARD | 0010655 |
| Is cancer (heuristic) | no |
Also known as: cone-rod dystrophy 5 · cone-rod dystrophy caused by mutation in PITPNM3 · cone-rod dystrophy type 5 · CORD5 · PITPNM3 cone-rod dystrophy
Data availability: 162 ClinVar variants · 2 GenCC gene-disease records.
Disease family
Classification path: disease › human disease › disease by body system or component › nervous system disorder › retinal disorder › retinal degeneration › inherited retinal dystrophy › cone-rod dystrophy › cone-rod dystrophy 5
Related subtypes (27): cone-rod dystrophy 2, macular degeneration, X-linked atrophic, cone-rod dystrophy 1, cone-rod dystrophy 6, cone dystrophy 3, cone-rod dystrophy 7, cone-rod dystrophy 3, Leber congenital amaurosis 4, cone-rod dystrophy 8, Newfoundland cone-rod dystrophy, cone-rod dystrophy 13, cone-rod dystrophy 10, cone-rod dystrophy 11, retinal cone dystrophy 4, cone-rod dystrophy 12, cone-rod dystrophy 9, cone-rod dystrophy 15, cone-rod dystrophy 16, cone-rod dystrophy 17, cone-rod dystrophy 18, cone-rod dystrophy 19, cone-rod dystrophy 20, cone-rod dystrophy 21, X-linked cone-rod dystrophy, cone-rod dystrophy 22, cone-rod dystrophy 14, cone-rod dystrophy 24
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
162 retrieved; paginated sample, class counts are floors:
75 uncertain significance, 48 benign, 25 conflicting classifications of pathogenicity, 10 benign/likely benign, 4 likely benign
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 167471 | NM_031220.4(PITPNM3):c.1124C>T (p.Pro375Leu) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 194272 | NM_031220.4(PITPNM3):c.1688C>T (p.Thr563Met) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 194895 | NM_031220.4(PITPNM3):c.2355G>A (p.Pro785=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 198270 | NM_031220.4(PITPNM3):c.507C>A (p.Phe169Leu) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 199174 | NM_031220.4(PITPNM3):c.987G>A (p.Leu329=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 1994 | NM_031220.4(PITPNM3):c.1878G>C (p.Gln626His) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324747 | NM_031220.4(PITPNM3):c.1899G>A (p.Thr633=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324748 | NM_031220.4(PITPNM3):c.1854G>A (p.Glu618=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324751 | NM_031220.4(PITPNM3):c.1538G>A (p.Arg513His) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324755 | NM_031220.4(PITPNM3):c.1019G>A (p.Arg340Gln) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324757 | NM_031220.4(PITPNM3):c.914C>T (p.Ala305Val) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324760 | NM_031220.4(PITPNM3):c.747G>A (p.Lys249=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324762 | NM_031220.4(PITPNM3):c.456C>A (p.Ala152=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324763 | NM_031220.4(PITPNM3):c.368G>A (p.Arg123His) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324769 | NM_031220.4(PITPNM3):c.195C>T (p.Ile65=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 324772 | NM_031220.4(PITPNM3):c.22+15G>C | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 838018 | NM_031220.4(PITPNM3):c.2190G>A (p.Thr730=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 839720 | NM_031220.4(PITPNM3):c.287G>A (p.Arg96Gln) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 888971 | NM_031220.4(PITPNM3):c.1018C>T (p.Arg340Trp) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 889652 | NM_031220.4(PITPNM3):c.853G>A (p.Asp285Asn) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 889654 | NM_031220.4(PITPNM3):c.651C>T (p.Ala217=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 890612 | NM_031220.4(PITPNM3):c.1942C>T (p.Pro648Ser) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 891165 | NM_031220.4(PITPNM3):c.1608C>T (p.Pro536=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 892364 | NM_031220.4(PITPNM3):c.1377C>T (p.Ser459=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 892365 | NM_031220.4(PITPNM3):c.1314C>T (p.Asp438=) | PITPNM3 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 888912 | NM_031220.4(PITPNM3):c.*54G>A | LOC130060086 | Uncertain significance | criteria provided, single submitter |
| 1032920 | NM_031220.4(PITPNM3):c.2305C>T (p.Arg769Trp) | PITPNM3 | Uncertain significance | criteria provided, single submitter |
| 1305959 | NM_031220.4(PITPNM3):c.2166G>C (p.Gln722His) | PITPNM3 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 324652 | NM_031220.4(PITPNM3):c.*4047C>T | PITPNM3 | Uncertain significance | criteria provided, single submitter |
| 324655 | NM_031220.4(PITPNM3):c.*3707G>A | PITPNM3 | Uncertain significance | criteria provided, single submitter |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 3 · Orphanet: 1 · 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 |
|---|---|---|---|---|
| PITPNM3 | Strong | Autosomal dominant | cone-rod dystrophy 5 | 3 |
Orphanet rare-disease linkage (cohort genes)
| Gene | Orphanet ID | Rare disease |
|---|---|---|
| PITPNM3 | Orphanet:1872 | Cone rod dystrophy |
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 |
|---|---|---|---|---|---|
| PITPNM3 | HGNC:21043 | ENSG00000091622 | Q9BZ71 | Membrane-associated phosphatidylinositol transfer protein 3 | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| PITPNM3 | Membrane-associated phosphatidylinositol transfer protein 3 | Catalyzes the transfer of phosphatidylinositol and phosphatidylcholine between membranes (in vitro). |
Protein-family classification
Druggable: 0 · Difficult: 0 · Unknown: 1 · 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 |
|---|---|---|---|
| Other/Unknown | 1 | 1.8× | 0.558 |
Per-gene assignment
| Symbol | Family | Druggable? | EC | InterPro (top 3) |
|---|---|---|---|---|
| PITPNM3 | Other/Unknown | no | PI_transfer, DDHD_dom, HAD_sf |
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 |
|---|---|
| Brodmann (1909) area 23 | 1 |
| endothelial cell | 1 |
| pancreatic ductal cell | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| PITPNM3 | 222 | broad | marker | pancreatic ductal cell, endothelial cell, Brodmann (1909) area 23 |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| PITPNM3 | 817 |
Structural data
PDB: 1 · AlphaFold-only: 0 · No structure: 0
Cohort genes with PDB structures (top 30)
| Symbol | UniProt | PDB entries |
|---|---|---|
| PITPNM3 | Q9BZ71 | 1 |
Function
Pathway analysis
Distinct Reactome pathways touched by cohort: 1. 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 |
|---|---|---|---|---|
| Synthesis of PI | 1 | 2284.0× | 4e-04 | PITPNM3 |
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 |
|---|---|---|---|---|
| phosphatidylinositol biosynthetic process | 1 | 366.4× | 0.003 | PITPNM3 |
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 |
|---|---|---|
| PITPNM3 | 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 | PITPNM3 |
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) |
|---|---|---|
| PITPNM3 | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: PITPNM3