Retinitis pigmentosa 61

disease

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Also known as CLRN1 retinitis pigmentosaretinitis pigmentosa caused by mutation in CLRN1retinitis pigmentosa type 61RP61

Summary

Retinitis pigmentosa 61 (MONDO:0013610) is a disease caused by CLRN1 (GenCC Strong), with 2 cohort genes.

At a glance

Causal gene: CLRN1 (GenCC Strong)
Cohort genes: 2
ClinVar variants: 53

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	retinitis pigmentosa 61
Mondo ID	MONDO:0013610
OMIM	614180
DOID	DOID:0110373
UMLS	C3280041
MedGen	481671
GARD	0015766
Is cancer (heuristic)	no

Also known as: CLRN1 retinitis pigmentosa · retinitis pigmentosa 61 · retinitis pigmentosa caused by mutation in CLRN1 · retinitis pigmentosa type 61 · RP61

Data availability: 53 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 › retinitis pigmentosa › retinitis pigmentosa 61

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

53 retrieved; paginated sample, class counts are floors:

20 pathogenic/likely pathogenic, 18 likely pathogenic, 8 pathogenic, 5 uncertain significance, 2 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
1075882	NM_174878.3(CLRN1):c.31dup (p.Cys11fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1275768	NM_174878.3(CLRN1):c.148_149insTGTC (p.Ser50fs)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
1331448	NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1455146	NM_174878.3(CLRN1):c.513T>A (p.Tyr171Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
188726	NM_001195794.1(CLRN1):c.149_152delinsTGTCCAAT (p.Ser50fs)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
188875	NM_174878.3(CLRN1):c.502dup (p.Ile168fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1966493	NM_174878.3(CLRN1):c.190G>C (p.Gly64Arg)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1971725	NM_174878.3(CLRN1):c.591del (p.Phe197fs)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
2040098	NM_174878.3(CLRN1):c.528T>A (p.Tyr176Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2203455	NM_174878.3(CLRN1):c.149C>A (p.Ser50Ter)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
2680840	NM_174878.3(CLRN1):c.95T>A (p.Leu32Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2680846	NM_174878.3(CLRN1):c.555T>A (p.Tyr185Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2745158	NM_174878.3(CLRN1):c.138del (p.Val47fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
30575	NM_174878.3(CLRN1):c.92C>T (p.Pro31Leu)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
3241183	NM_174878.3(CLRN1):c.190_200dup (p.His67fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
371628	NM_174878.3(CLRN1):c.619C>T (p.Arg207Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
4392	NM_052995.2(CLRN1):c.300T>G (p.Tyr100Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
4395	NM_174878.3(CLRN1):c.144T>G (p.Asn48Lys)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
4397	NM_174878.3(CLRN1):c.189C>A (p.Tyr63Ter)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
48142	NM_174878.3(CLRN1):c.127G>A (p.Gly43Arg)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
48145	NM_174878.3(CLRN1):c.301_305del (p.Val101fs)	CLRN1	Pathogenic	criteria provided, multiple submitters, no conflicts
48146	NM_174878.3(CLRN1):c.368C>A (p.Ala123Asp)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
552163	NM_174878.3(CLRN1):c.541C>T (p.Gln181Ter)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
638640	NM_174878.3(CLRN1):c.433+1G>A	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
644615	NM_174878.3(CLRN1):c.578del (p.Phe193fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
651716	NM_174878.3(CLRN1):c.121_136dup (p.Leu46fs)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
971183	NM_174878.3(CLRN1):c.606T>G (p.Asn202Lys)	CLRN1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
30574	NM_174878.3(CLRN1):c.461T>G (p.Leu154Trp)	CLRN1-AS1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1511878	NM_174878.3(CLRN1):c.253+1G>A	CLRN1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
2680841	NM_174878.3(CLRN1):c.129del (p.Ala44fs)	CLRN1	Likely pathogenic	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · Orphanet: 2 · 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
CLRN1	Strong	Autosomal recessive	retinitis pigmentosa 61	7

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
CLRN1	Orphanet:231183	Usher syndrome type 3
CLRN1	Orphanet:791	Retinitis pigmentosa

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
CLRN1	HGNC:12605	ENSG00000163646	P58418	Clarin-1	gencc,clinvar
SIAH2-AS1	HGNC:40526	ENSG00000244265		SIAH2 and CLRN1 antisense RNA 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CLRN1	Clarin-1	May have a role in the excitatory ribbon synapse junctions between hair cells and cochlear ganglion cells and presumably also in analogous synapses within the retina.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · 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	2	1.8×	0.312

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CLRN1	Other/Unknown	no		Clarin
SIAH2-AS1	Other/Unknown	no

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)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
adrenal tissue	1
right adrenal gland	1
right adrenal gland cortex	1
buccal mucosa cell	1
oocyte	1
secondary oocyte	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CLRN1	61	tissue_specific	marker	adrenal tissue, right adrenal gland cortex, right adrenal gland
SIAH2-AS1	161	broad	yes	secondary oocyte, oocyte, buccal mucosa cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CLRN1	727
SIAH2-AS1	0

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CLRN1	P58418	90.74

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 2 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
equilibrioception	1	2407.4×	0.002	CLRN1
sensory perception of light stimulus	1	1872.4×	0.002	CLRN1
auditory receptor cell stereocilium organization	1	842.6×	0.004	CLRN1
positive regulation of lamellipodium assembly	1	601.9×	0.004	CLRN1
cell motility	1	401.2×	0.004	CLRN1
photoreceptor cell maintenance	1	358.6×	0.004	CLRN1
actin filament organization	1	118.7×	0.011	CLRN1
sensory perception of sound	1	100.9×	0.011	CLRN1
visual perception	1	79.5×	0.013	CLRN1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 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
CLRN1	0	0
SIAH2-AS1	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	2	CLRN1, SIAH2-AS1

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
CLRN1	0	—
SIAH2-AS1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: CLRN1, SIAH2-AS1