intellectual developmental disorder and retinitis pigmentosa; IDDRP

Summary

intellectual developmental disorder and retinitis pigmentosa; IDDRP (MONDO:0032594) is a disease caused by SCAPER (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: SCAPER (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 46

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	intellectual developmental disorder and retinitis pigmentosa; IDDRP
Mondo ID	MONDO:0032594
OMIM	618195
UMLS	C4748658
MedGen	1648358
GARD	0016306
Is cancer (heuristic)	no

Also known as: IDDRP

Data availability: 46 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › neurodevelopmental disorder › intellectual disability › intellectual developmental disorder and retinitis pigmentosa; IDDRP

Related subtypes (9): syndromic intellectual disability, non-syndromic intellectual disability, PPP2R1A-related intellectual disability, intellectual disability, autosomal dominant, X-linked intellectual disability, intellectual disability, autosomal recessive, NACC1-related neurodevelopmental disorder with epilepsy, cataracts and episodic irritability, SETD2-related neurodevelopmental disorder without or with macrocephaly/overgrowth, intellectual developmental disorder with polymicrogyria and seizures

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

46 retrieved; paginated sample, class counts are floors:

15 likely pathogenic, 13 uncertain significance, 8 benign, 6 pathogenic, 2 pathogenic/likely pathogenic, 1 conflicting classifications of pathogenicity, 1 benign/likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
3544437	NM_020843.4(SCAPER):c.1461_1462insGTGGTATATCC (p.Met488fs)	SCAPER	Pathogenic	criteria provided, single submitter
417685	NM_020843.3(SCAPER):c.2973_2976del (p.Ile991Metfs)	SCAPER	Pathogenic	criteria provided, single submitter
424861	NM_020843.4(SCAPER):c.2023-2A>G	SCAPER	Pathogenic	no assertion criteria provided
427855	NM_020843.4(SCAPER):c.3656G>A (p.Ser1219Asn)	SCAPER	Pathogenic/Likely pathogenic	no assertion criteria provided
427856	NM_020843.3(SCAPER):c.1859_1861del (p.Glu620del)	SCAPER	Pathogenic/Likely pathogenic	no assertion criteria provided
620525	NM_020843.4(SCAPER):c.2377C>T (p.Gln793Ter)	SCAPER	Pathogenic	criteria provided, single submitter
800544	NM_020843.4(SCAPER):c.2236dup (p.Ile746fs)	SCAPER	Pathogenic	criteria provided, single submitter
800545	NM_020843.4(SCAPER):c.2179C>T (p.Arg727Ter)	SCAPER	Pathogenic	criteria provided, single submitter
800548	NM_020843.4(SCAPER):c.3224del (p.Pro1075fs)	LOC126862183	Likely pathogenic	no assertion criteria provided
1325035	NM_020843.4(SCAPER):c.2961_2962del (p.Cys988fs)	SCAPER	Likely pathogenic	criteria provided, single submitter
1325036	NM_020843.4(SCAPER):c.2955-1G>T	SCAPER	Likely pathogenic	criteria provided, single submitter
1334384	NM_020843.4(SCAPER):c.334C>T (p.Arg112Ter)	SCAPER	Likely pathogenic	criteria provided, single submitter
1676479	NM_020843.4(SCAPER):c.125-1G>A	SCAPER	Likely pathogenic	criteria provided, single submitter
3065980	NM_020843.4(SCAPER):c.2364T>A (p.Tyr788Ter)	SCAPER	Likely pathogenic	criteria provided, single submitter
3248655	NM_020843.4(SCAPER):c.2613dup (p.Ala872fs)	SCAPER	Likely pathogenic	criteria provided, single submitter
4087726	NM_020843.4(SCAPER):c.2605A>T (p.Lys869Ter)	SCAPER	Likely pathogenic	criteria provided, single submitter
800546	NM_020843.4(SCAPER):c.1116del (p.Val373fs)	SCAPER	Likely pathogenic	no assertion criteria provided
800547	NM_020843.4(SCAPER):c.1495+1G>A	SCAPER	Likely pathogenic	no assertion criteria provided
800549	NM_020843.4(SCAPER):c.829C>T (p.Arg277Ter)	SCAPER	Likely pathogenic	no assertion criteria provided
800550	NM_020843.4(SCAPER):c.3707_3708del (p.Ser1236fs)	SCAPER	Likely pathogenic	no assertion criteria provided
800551	NM_020843.4(SCAPER):c.2166-3C>G	SCAPER	Likely pathogenic	no assertion criteria provided
829945	NM_020843.4(SCAPER):c.2653del (p.Glu885fs)	SCAPER	Likely pathogenic	no assertion criteria provided
829946	NM_020843.4(SCAPER):c.1081C>T (p.Arg361Ter)	SCAPER	Likely pathogenic	criteria provided, single submitter
2400307	NM_020843.4(SCAPER):c.3431A>G (p.His1144Arg)	SCAPER	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2595022	NM_020843.4(SCAPER):c.3113G>A (p.Gly1038Glu)	LOC126862183	Uncertain significance	criteria provided, multiple submitters, no conflicts
1184367	NM_020843.4(SCAPER):c.3065T>C (p.Ile1022Thr)	SCAPER	Uncertain significance	criteria provided, single submitter
1727209	NM_020843.4(SCAPER):c.213T>G (p.Cys71Trp)	SCAPER	Uncertain significance	criteria provided, single submitter
2435661	NM_020843.4(SCAPER):c.1883T>C (p.Phe628Ser)	SCAPER	Uncertain significance	criteria provided, single submitter
2435662	NM_020843.4(SCAPER):c.1382A>T (p.Asp461Val)	SCAPER	Uncertain significance	criteria provided, single submitter
2435663	NM_020843.4(SCAPER):c.1250C>T (p.Ser417Phe)	SCAPER	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · 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
SCAPER	Strong	Autosomal recessive	intellectual developmental disorder and retinitis pigmentosa; IDDRP	6

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SCAPER	Orphanet:110	Bardet-Biedl syndrome
SCAPER	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
SCAPER	HGNC:13081	ENSG00000140386	Q9BY12	S phase cyclin A-associated protein in the endoplasmic reticulum	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SCAPER	S phase cyclin A-associated protein in the endoplasmic reticulum	CCNA2/CDK2 regulatory protein that transiently maintains CCNA2 in the cytoplasm.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · 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
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SCAPER	Transcription factor	no		Matrin/U1-like-C_Znf_C2H2, Znf_C2H2_type, SCAPER_N

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
cortical plate	1
male germ line stem cell (sensu Vertebrata) in testis	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SCAPER	282	ubiquitous	marker	cortical plate, male germ line stem cell (sensu Vertebrata) in testis, sural nerve

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SCAPER	711

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SCAPER	Q9BY12	2

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
antral ovarian follicle growth	1	3370.4×	0.001	SCAPER
seminiferous tubule development	1	766.0×	0.003	SCAPER
retina development in camera-type eye	1	255.3×	0.005	SCAPER
spermatogenesis	1	35.2×	0.028	SCAPER

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
SCAPER	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	SCAPER

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)
SCAPER	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.