spondyloepimetaphyseal dysplasia, Isidor-Toutain type

disease

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Also known as SEMDIST

Summary

spondyloepimetaphyseal dysplasia, Isidor-Toutain type (MONDO:0032885) is a disease caused by RPL13 (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: RPL13 (GenCC Strong)
Cohort genes: 1
ClinVar variants: 17

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	spondyloepimetaphyseal dysplasia, Isidor-Toutain type
Mondo ID	MONDO:0032885
OMIM	618728
UMLS	C5231478
MedGen	1684771
GARD	0027137
Is cancer (heuristic)	no

Also known as: SEMDIST

Data availability: 17 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › skeletal system disorder › bone disorder › bone development disease › osteochondrodysplasia › spondyloepimetaphyseal dysplasia › spondyloepimetaphyseal dysplasia, Isidor-Toutain type

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

17 retrieved; paginated sample, class counts are floors:

5 pathogenic, 5 uncertain significance, 2 conflicting classifications of pathogenicity, 2 benign, 2 likely pathogenic, 1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
2671824	NM_000977.4(RPL13):c.478-1G>T	RPL13	Pathogenic	criteria provided, single submitter
689800	NM_000977.4(RPL13):c.477+1G>T	RPL13	Pathogenic	criteria provided, single submitter
689801	NM_000977.4(RPL13):c.477+2T>C	RPL13	Pathogenic	no assertion criteria provided
689802	NM_000977.4(RPL13):c.477+1G>A	RPL13	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
813853	NM_000977.4(RPL13):c.533C>A (p.Ala178Asp)	RPL13	Pathogenic	no assertion criteria provided
813854	NM_000977.4(RPL13):c.553G>C (p.Ala185Pro)	RPL13	Pathogenic	no assertion criteria provided
1696793	NM_000977.4(RPL13):c.569G>T (p.Arg190Leu)	RPL13	Likely pathogenic	criteria provided, single submitter
3362462	NM_000977.4(RPL13):c.516dup (p.Glu173fs)	RPL13	Likely pathogenic	criteria provided, single submitter
1030926	NM_000977.4(RPL13):c.548G>A (p.Arg183His)	RPL13	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
804147	NM_000977.4(RPL13):c.548G>C (p.Arg183Pro)	RPL13	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3731329	NM_000977.4(RPL13):c.538G>T (p.Ala180Ser)	RPL13	Uncertain significance	criteria provided, single submitter
4075375	NM_000977.4(RPL13):c.569G>C (p.Arg190Pro)	RPL13	Uncertain significance	criteria provided, single submitter
4278355	NM_000977.4(RPL13):c.484A>G (p.Lys162Glu)	RPL13	Uncertain significance	criteria provided, single submitter
4293081	NM_000977.4(RPL13):c.504_507dup (p.Thr170fs)	RPL13	Uncertain significance	criteria provided, single submitter
4531629	NM_000977.4(RPL13):c.184C>A (p.Pro62Thr)	RPL13	Uncertain significance	criteria provided, single submitter
1327970	NM_000977.4(RPL13):c.93T>G (p.Arg31=)	LOC130059823	Benign	criteria provided, multiple submitters, no conflicts
1327971	NM_000977.4(RPL13):c.141C>T (p.Ala47=)	LOC130059824	Benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · 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
RPL13	Strong	Autosomal dominant	spondyloepimetaphyseal dysplasia, Isidor-Toutain type	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
RPL13	Orphanet:370015	Spondyloepimetaphyseal dysplasia, Isidor-Toutain type

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
RPL13	HGNC:10303	ENSG00000167526	P26373	Large ribosomal subunit protein eL13	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
RPL13	Large ribosomal subunit protein eL13	Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell.

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)
RPL13	Other/Unknown	no		Ribosomal_eL13, Ribosomal_eL13_CS

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
left ovary	1
right ovary	1
right uterine tube	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
RPL13	311	ubiquitous	marker	right uterine tube, right ovary, left ovary

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
RPL13	4,612

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
RPL13	P26373	191

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 16. 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
Peptide chain elongation	1	126.9×	0.012	RPL13
Viral mRNA Translation	1	126.9×	0.012	RPL13
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	1	125.5×	0.012	RPL13
Selenocysteine synthesis	1	120.2×	0.012	RPL13
Eukaryotic Translation Termination	1	120.2×	0.012	RPL13
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	1	117.7×	0.012	RPL13
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	1	117.7×	0.012	RPL13
Formation of a pool of free 40S subunits	1	112.0×	0.012	RPL13
Response of EIF2AK4 (GCN2) to amino acid deficiency	1	110.9×	0.012	RPL13
Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide	1	106.7×	0.012	RPL13
L13a-mediated translational silencing of Ceruloplasmin expression	1	101.1×	0.012	RPL13
SRP-dependent cotranslational protein targeting to membrane	1	100.2×	0.012	RPL13
GTP hydrolysis and joining of the 60S ribosomal subunit	1	100.2×	0.012	RPL13
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	1	97.6×	0.012	RPL13
Regulation of expression of SLITs and ROBOs	1	69.2×	0.015	RPL13
Major pathway of rRNA processing in the nucleolus and cytosol	1	61.7×	0.016	RPL13

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
blastocyst development	1	674.1×	0.006	RPL13
bone development	1	276.3×	0.007	RPL13
cytoplasmic translation	1	185.2×	0.007	RPL13
translation	1	102.8×	0.010	RPL13

Therapeutics

Drug target analysis

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

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

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

Symbol	Example approved molecule
RPL13	GENTAMICIN SULFATE

Top cohort targets by molecule count

Symbol	Molecules	Max phase
RPL13	1	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
GENTAMICIN SULFATE	4	RPL13

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

Symbol	Assays	Type breakdown
RPL13	90	Binding:90

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

1 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.

Compound	Max phase	Cohort target (bioactivity)
GENTAMICIN SULFATE	4	RPL13

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	RPL13
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	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: RPL13