Retinitis pigmentosa 90

disease

On this page

Also known as RP90

Summary

Retinitis pigmentosa 90 (MONDO:0033563) is a disease caused by IDH3A (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: IDH3A (GenCC Strong)
Cohort genes: 1
ClinVar variants: 14

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	retinitis pigmentosa 90
Mondo ID	MONDO:0033563
OMIM	619007
DOID	DOID:0112147
UMLS	C5436588
MedGen	1733837
GARD	0025810
Is cancer (heuristic)	no

Also known as: RP90

Data availability: 14 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 90

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

14 retrieved; paginated sample, class counts are floors:

6 pathogenic, 5 uncertain significance, 3 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
977468	NM_005530.3(IDH3A):c.716T>C (p.Met239Thr)	IDH3A	Pathogenic	no assertion criteria provided
977469	NM_005530.3(IDH3A):c.403del (p.Thr135fs)	IDH3A	Pathogenic	criteria provided, single submitter
977470	NM_005530.3(IDH3A):c.524C>T (p.Ala175Val)	IDH3A	Pathogenic	no assertion criteria provided
977471	NM_005530.3(IDH3A):c.463G>T (p.Gly155Ter)	IDH3A	Pathogenic	criteria provided, single submitter
977472	NM_005530.3(IDH3A):c.946C>T (p.Arg316Cys)	IDH3A	Pathogenic	criteria provided, single submitter
977473	NM_005530.3(IDH3A):c.612G>A (p.Met204Ile)	IDH3A	Pathogenic	no assertion criteria provided
812331	NM_005530.3(IDH3A):c.911C>A (p.Pro304His)	IDH3A	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
812332	NM_005530.3(IDH3A):c.938T>C (p.Met313Thr)	IDH3A	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
977474	NM_005530.3(IDH3A):c.364G>A (p.Ala122Thr)	IDH3A	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1366668	NM_005530.3(IDH3A):c.1081C>T (p.Arg361Ter)	IDH3A	Uncertain significance	criteria provided, multiple submitters, no conflicts
1462521	NM_005530.3(IDH3A):c.937A>C (p.Met313Leu)	IDH3A	Uncertain significance	criteria provided, multiple submitters, no conflicts
1803191	NM_005530.3(IDH3A):c.805G>A (p.Gly269Ser)	IDH3A	Uncertain significance	criteria provided, single submitter
3383362	NM_005530.3(IDH3A):c.532C>T (p.Arg178Cys)	IDH3A	Uncertain significance	criteria provided, single submitter
4294090	NM_005530.3(IDH3A):c.273C>A (p.Asn91Lys)	IDH3A	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
IDH3A	Strong	Autosomal recessive	retinitis pigmentosa 90	3

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
IDH3A	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
IDH3A	HGNC:5384	ENSG00000166411	P50213	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
IDH3A	Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial	Catalytic subunit of the enzyme which catalyzes the decarboxylation of isocitrate (ICT) into alpha-ketoglutarate.

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
Enzyme (other)	1	12.0×	0.083

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
IDH3A	Enzyme (other)	yes	1.1.1.41	Isocitrate_DH_NAD, IsoCit/isopropylmalate_DH_CS, IsoPropMal-DH-like_dom

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
heart left ventricle	1
heart right ventricle	1
right atrium auricular region	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
IDH3A	294	ubiquitous	marker	right atrium auricular region, heart right ventricle, heart left ventricle

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
IDH3A	3,215

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
IDH3A	P50213	19

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. 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
Citric acid cycle (TCA cycle)	1	423.0×	0.005	IDH3A
Mitochondrial protein degradation	1	114.2×	0.009	IDH3A

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
isocitrate metabolic process	1	3370.4×	9e-04	IDH3A
tricarboxylic acid cycle	1	510.7×	0.003	IDH3A
carbohydrate metabolic process	1	135.9×	0.007	IDH3A

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
IDH3A	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
IDH3A	2	Binding:2

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
IDH3A	1.1.1.41	isocitrate dehydrogenase (NAD+)

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	1	IDH3A
D	Druggable family + AlphaFold only, no drug	0
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)
IDH3A	2	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: IDH3A