Retinitis pigmentosa 41

Summary

Retinitis pigmentosa 41 (MONDO:0012796) is a disease caused by PROM1 (GenCC Definitive), with 1 cohort gene.

At a glance

• Causal gene: PROM1 (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 50

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	retinitis pigmentosa 41
Mondo ID	MONDO:0012796
MeSH	C567422
OMIM	612095
DOID	DOID:0110376
UMLS	C2677516
MedGen	383126
GARD	0010379
Is cancer (heuristic)	no

Also known as: PROM1 retinitis pigmentosa · retinitis pigmentosa 41 · retinitis pigmentosa caused by mutation in PROM1 · retinitis pigmentosa type 41 · RP 41 · RP41

Data availability: 50 ClinVar variants · 3 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 › retinitis pigmentosa › retinitis pigmentosa 41

Related subtypes (101): retinitis pigmentosa 6, cone-rod dystrophy 2, retinitis pigmentosa 1, retinitis pigmentosa 9, retinitis pigmentosa 10, dominant pericentral pigmentary retinopathy, late-adult onset retinitis pigmentosa, autosomal recessive pericentral pigmentary retinopathy, retinitis pigmentosa 3, retinitis pigmentosa 24, retinitis pigmentosa 23, retinitis pigmentosa 34, retinitis pigmentosa 2, retinitis pigmentosa Y-linked, retinitis pigmentosa 13, retinitis pigmentosa 12, retinitis pigmentosa 14, retinitis pigmentosa 11, retinitis pigmentosa 17, retinitis pigmentosa 18, retinitis pigmentosa 19, retinitis pigmentosa 22, retinitis pigmentosa 25, retinitis pigmentosa 28, retinitis pigmentosa 30, retinitis pigmentosa 7, retinitis pigmentosa 26, retinitis pigmentosa 32, retinitis pigmentosa 31, retinitis pigmentosa 35, retinitis pigmentosa 33, retinitis pigmentosa 36, retinitis pigmentosa 37, retinitis pigmentosa 29, retinitis pigmentosa 46, retinitis pigmentosa 42, retinitis pigmentosa 50, retinitis pigmentosa 54, retinitis pigmentosa 51, retinitis pigmentosa 55, retinitis pigmentosa 56, retinitis pigmentosa 57, retinitis pigmentosa 58, cone-rod dystrophy 15, retinitis pigmentosa 4, retinitis pigmentosa 27, retinitis pigmentosa 49, retinitis pigmentosa 47, retinitis pigmentosa 45, retinitis pigmentosa 44, retinitis pigmentosa 20, retinitis pigmentosa 40, retinitis pigmentosa 39, retinitis pigmentosa 43, retinitis pigmentosa 48, retinitis pigmentosa 59, retinitis pigmentosa 38, retinitis pigmentosa 60, retinitis pigmentosa 61, retinitis pigmentosa 62, retinitis pigmentosa 63, cone-rod dystrophy 16, retinitis pigmentosa 66, retinitis pigmentosa with or without situs inversus, retinitis pigmentosa 67, retinitis pigmentosa 68, retinitis pigmentosa 69, retinitis pigmentosa 70, retinal dystrophy and obesity, retinitis pigmentosa 71, retinitis pigmentosa 72, retinitis pigmentosa 73, retinitis pigmentosa 74, retinitis pigmentosa 75, retinitis pigmentosa 76, retinitis pigmentosa 77, retinitis pigmentosa 92, retinitis pigmentosa 93, retinitis pigmentosa 83, retinitis pigmentosa 84, retinitis pigmentosa 85, retinitis pigmentosa 86, retinitis pigmentosa 87 with choroidal involvement, retinitis pigmentosa 88, retinitis pigmentosa 90, retinitis pigmentosa 81, retinitis pigmentosa 78, retinitis pigmentosa 79, retinitis pigmentosa 80, retinitis pigmentosa 94, variable age at onset, retinitis pigmentosa 53, retinitis pigmentosa 65, retinitis pigmentosa 64, retinitis pigmentosa 95, retinitis pigmentosa 96, retinitis pigmentosa 97, retinitis pigmentosa 98, retinitis pigmentosa 99, retinitis pigmentosa 100, retinitis pigmentosa 101, retinitis pigmentosa 7, digenic

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

50 retrieved; paginated sample, class counts are floors:

11 pathogenic, 10 pathogenic/likely pathogenic, 10 uncertain significance, 7 conflicting classifications of pathogenicity, 6 likely pathogenic, 5 benign, 1 benign/likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
1070960	NM_006017.3(PROM1):c.2023C>T (p.Gln675Ter)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
1213882	NM_006017.3(PROM1):c.1956T>G (p.Tyr652Ter)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
208605	NM_006017.3(PROM1):c.1177_1178del (p.Ile393fs)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
372711	NM_006017.3(PROM1):c.1354dup (p.Tyr452fs)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
3780492	NM_006017.3(PROM1):c.154del (p.Ile52fs)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
402237	NM_006017.3(PROM1):c.622del (p.Thr208fs)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
438214	NM_006017.3(PROM1):c.436C>T (p.Arg146Ter)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
4537472	NM_006017.3(PROM1):c.1850dup (p.Asn617fs)	PROM1	Pathogenic	criteria provided, single submitter
5608	NM_006017.3(PROM1):c.1841del (p.Gly614fs)	PROM1	Pathogenic	no assertion criteria provided
5609	NM_006017.3(PROM1):c.1726C>T (p.Gln576Ter)	PROM1	Pathogenic	criteria provided, single submitter
5610	NM_006017.3(PROM1):c.1117C>T (p.Arg373Cys)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
623211	NM_006017.3(PROM1):c.1301+2T>C	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
634483	NM_006017.3(PROM1):c.2050C>T (p.Arg684Ter)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
694038	NM_006017.3(PROM1):c.139del (p.His47fs)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
802053	NM_006017.3(PROM1):c.1984-1G>T	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
802055	NM_006017.3(PROM1):c.869del (p.Ser290fs)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
802056	NM_006017.3(PROM1):c.784+1G>A	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
802057	NM_006017.3(PROM1):c.652C>T (p.Gln218Ter)	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
809626	NM_006017.3(PROM1):c.1142-1G>A	PROM1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
936195	NM_006017.3(PROM1):c.1500del (p.Ile500fs)	PROM1	Pathogenic	criteria provided, multiple submitters, no conflicts
965933	NM_006017.3(PROM1):c.1682+3A>G	PROM1	Pathogenic	criteria provided, single submitter
1333399	NM_006017.3(PROM1):c.2209G>T (p.Glu737Ter)	PROM1	Likely pathogenic	criteria provided, single submitter
1333451	NM_006017.3(PROM1):c.276+2T>C	PROM1	Likely pathogenic	criteria provided, single submitter
2920640	NM_006017.3(PROM1):c.1883_1884del (p.Arg628fs)	PROM1	Likely pathogenic	no assertion criteria provided
3066383	NM_006017.3(PROM1):c.509+1G>A	PROM1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
3776076	NM_006017.3(PROM1):c.1356C>A (p.Tyr452Ter)	PROM1	Likely pathogenic	criteria provided, single submitter
965934	NM_006017.3(PROM1):c.2281-2A>G	PROM1	Likely pathogenic	criteria provided, single submitter
191189	NM_006017.3(PROM1):c.604C>G (p.Arg202Gly)	PROM1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
194072	NM_006017.3(PROM1):c.1345G>A (p.Val449Met)	PROM1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
236524	NM_006017.3(PROM1):c.1632G>T (p.Gly544=)	PROM1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 10 · Orphanet: 4 · 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
PROM1	Definitive	Autosomal recessive	retinitis pigmentosa 41	10

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PROM1	Orphanet:1872	Cone rod dystrophy
PROM1	Orphanet:319640	Retinal macular dystrophy type 2
PROM1	Orphanet:791	Retinitis pigmentosa
PROM1	Orphanet:827	Stargardt disease

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
PROM1	HGNC:9454	ENSG00000007062	O43490	Prominin-1	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PROM1	Prominin-1	May play a role in cell differentiation, proliferation and apoptosis.

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)
PROM1	Other/Unknown	no		Prominin

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
bronchial epithelial cell	1
bronchus	1
epithelium of bronchus	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PROM1	252	broad	marker	bronchial epithelial cell, epithelium of bronchus, bronchus

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PROM1	3,302

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
PROM1	O43490	85.68

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
Developmental Lineage of Pancreatic Ductal Cells	1	228.4×	0.004	PROM1

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
glomerular parietal epithelial cell differentiation	1	8426.0×	6e-04	PROM1
positive regulation of nephron tubule epithelial cell differentiation	1	5617.3×	6e-04	PROM1
camera-type eye photoreceptor cell differentiation	1	3370.4×	7e-04	PROM1
retina morphogenesis in camera-type eye	1	1872.4×	9e-04	PROM1
podocyte differentiation	1	1404.3×	1e-03	PROM1
retina layer formation	1	648.1×	0.002	PROM1
photoreceptor cell maintenance	1	358.6×	0.003	PROM1

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
PROM1	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	PROM1

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)
PROM1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.