Retinitis pigmentosa 93

Summary

Retinitis pigmentosa 93 (MONDO:0030797) is a disease caused by CC2D2A (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: CC2D2A (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 270

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	retinitis pigmentosa 93
Mondo ID	MONDO:0030797
OMIM	619845
DOID	DOID:0061105
UMLS	C5676970
MedGen	1810905
GARD	0025638
Is cancer (heuristic)	no

Also known as: CC2D2A retinitis pigmentosa 93 · retinitis pigmentosa 93 · RP93

Data availability: 270 ClinVar variants · 1 GenCC gene-disease record.

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 93

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 41, 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 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

270 retrieved; paginated sample, class counts are floors:

147 uncertain significance, 38 pathogenic/likely pathogenic, 35 conflicting classifications of pathogenicity, 32 likely pathogenic, 15 pathogenic, 2 likely benign, 1 benign/likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
1074596	NM_001378615.1(CC2D2A):c.1538G>A (p.Trp513Ter)	CC2D2A	Pathogenic	criteria provided, multiple submitters, no conflicts
126242	NM_001378615.1(CC2D2A):c.394C>T (p.Arg132Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1297595	NM_001378615.1(CC2D2A):c.712G>T (p.Glu238Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1322034	NM_001378615.1(CC2D2A):c.3763C>T (p.Arg1255Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1395827	NM_001378615.1(CC2D2A):c.3688C>T (p.Arg1230Ter)	CC2D2A	Pathogenic	criteria provided, multiple submitters, no conflicts
1427276	NM_001378615.1(CC2D2A):c.4522del (p.Ile1508fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1456425	NM_001378615.1(CC2D2A):c.121C>T (p.Gln41Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
166801	NM_001378615.1(CC2D2A):c.1017+1G>A	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
1686896	NC_000004.12:g.15563877_15580021del	CC2D2A	Pathogenic	no assertion criteria provided
1686898	NM_001378615.1(CC2D2A):c.4730_4731delinsTGTATA (p.Ala1577fs)	CC2D2A	Pathogenic	no assertion criteria provided
1904397	NM_001378615.1(CC2D2A):c.3535G>T (p.Glu1179Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
210609	NM_001378615.1(CC2D2A):c.2683C>T (p.Gln895Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
210612	NM_001378615.1(CC2D2A):c.4465_4468del (p.Asp1489fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
217597	NM_001378615.1(CC2D2A):c.3850C>T (p.Arg1284Cys)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
217602	NM_001378615.1(CC2D2A):c.3055C>T (p.Arg1019Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
217604	NM_001378615.1(CC2D2A):c.2999A>T (p.Glu1000Val)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
217607	NM_001378615.1(CC2D2A):c.4667A>T (p.Asp1556Val)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2203534	NM_001378615.1(CC2D2A):c.2581G>A (p.Asp861Asn)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
289869	NM_001378615.1(CC2D2A):c.4179+1G>A	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2925185	NM_001378615.1(CC2D2A):c.463C>T (p.Gln155Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2934877	NM_001378615.1(CC2D2A):c.715del (p.Met239fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2936760	NM_001378615.1(CC2D2A):c.4522dup (p.Ile1508fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2938979	NM_001080522.2(CC2D2A):c.3597_3600del	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2940749	NM_001378615.1(CC2D2A):c.2923-1G>A	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2942128	NM_001378615.1(CC2D2A):c.839del (p.Gln280fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2954141	NM_001378615.1(CC2D2A):c.2568del (p.Glu857fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
3382631	NM_001378615.1(CC2D2A):c.3613dup (p.Ile1205fs)	CC2D2A	Pathogenic	criteria provided, single submitter
3590278	NM_001378615.1(CC2D2A):c.1363C>T (p.Gln455Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
3590387	NM_001378615.1(CC2D2A):c.3280del (p.Leu1094fs)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
411851	NM_001378615.1(CC2D2A):c.1267C>T (p.Arg423Ter)	CC2D2A	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 7 · 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
CC2D2A	Strong	Autosomal recessive	retinitis pigmentosa 93	7

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
CC2D2A	Orphanet:1454	Joubert syndrome with hepatic defect
CC2D2A	Orphanet:2318	Joubert syndrome with oculorenal defect
CC2D2A	Orphanet:564	Meckel syndrome
CC2D2A	Orphanet:791	Retinitis pigmentosa

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
CC2D2A	HGNC:29253	ENSG00000048342	Q9P2K1	Coiled-coil and C2 domain-containing protein 2A	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CC2D2A	Coiled-coil and C2 domain-containing protein 2A	Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes.

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
Protease	1	36.6×	0.027

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CC2D2A	Protease	yes		C2_dom, CC2D2AN-C2, C2_domain_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
bronchial epithelial cell	1
bronchus	1
right uterine tube	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CC2D2A	247	ubiquitous	marker	right uterine tube, bronchial epithelial cell, bronchus

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CC2D2A	899

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CC2D2A	Q9P2K1	69.46

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. 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
Anchoring of the basal body to the plasma membrane	1	113.1×	0.014	CC2D2A
Cilium Assembly	1	108.8×	0.014	CC2D2A
Organelle biogenesis and maintenance	1	66.0×	0.015	CC2D2A

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
protein localization to ciliary transition zone	1	2407.4×	0.005	CC2D2A
embryonic brain development	1	802.5×	0.006	CC2D2A
motile cilium assembly	1	581.1×	0.006	CC2D2A
axoneme assembly	1	543.6×	0.006	CC2D2A
camera-type eye development	1	358.6×	0.007	CC2D2A
non-motile cilium assembly	1	290.6×	0.007	CC2D2A
determination of left/right symmetry	1	255.3×	0.007	CC2D2A
neural tube closure	1	187.2×	0.007	CC2D2A
smoothened signaling pathway	1	181.2×	0.007	CC2D2A
kidney development	1	140.4×	0.009	CC2D2A
heart development	1	78.8×	0.014	CC2D2A
cilium assembly	1	73.6×	0.014	CC2D2A

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
CC2D2A	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	1	CC2D2A
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)
CC2D2A	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.