Short-rib thoracic dysplasia 16 with or without polydactyly

disease

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Also known as short-rib thoracic dysplasia 16 with or without polydactylySRTD16

Summary

Short-rib thoracic dysplasia 16 with or without polydactyly (MONDO:0014915) is a disease caused by IFT52 (GenCC Strong), with 1 cohort gene.

At a glance

Causal gene: IFT52 (GenCC Strong)
Cohort genes: 1
ClinVar variants: 9

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	short-rib thoracic dysplasia 16 with or without polydactyly
Mondo ID	MONDO:0014915
OMIM	617102
UMLS	C4310718
MedGen	934685
GARD	0016189
Is cancer (heuristic)	no

Also known as: short-rib thoracic dysplasia 16 with or without polydactyly · short-rib thoracic dysplasia 16 with or without polydactyly; SRTD16 · SRTD16

Data availability: 9 ClinVar variants · 5 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive disease › craniosynostosis syndrome, autosomal recessive › cranioectodermal dysplasia › short-rib thoracic dysplasia 16 with or without polydactyly

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

9 retrieved; paginated sample, class counts are floors:

4 pathogenic, 2 uncertain significance, 1 benign, 1 likely pathogenic, 1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
253306	NM_016004.5(IFT52):c.424C>T (p.Arg142Ter)	IFT52	Pathogenic	criteria provided, single submitter
253308	NM_016004.5(IFT52):c.878del (p.Leu293fs)	IFT52	Pathogenic/Likely pathogenic	no assertion criteria provided
983487	NM_016004.5(IFT52):c.695_699delinsCA (p.Ile232_Met233delinsThr)	IFT52	Pathogenic	no assertion criteria provided
983488	NM_016004.5(IFT52):c.556A>G (p.Thr186Ala)	IFT52	Pathogenic	no assertion criteria provided
983489	NM_016004.5(IFT52):c.293A>G (p.Asn98Ser)	IFT52	Pathogenic	no assertion criteria provided
253307	NM_016004.5(IFT52):c.595G>A (p.Ala199Thr)	IFT52	Likely pathogenic	criteria provided, single submitter
1427662	NM_016004.5(IFT52):c.157G>A (p.Val53Met)	IFT52	Uncertain significance	criteria provided, multiple submitters, no conflicts
1683682	NM_016004.5(IFT52):c.1189C>T (p.Pro397Ser)	IFT52	Uncertain significance	criteria provided, multiple submitters, no conflicts
1183241	NM_016004.5(IFT52):c.159G>A (p.Val53=)	IFT52	Benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · 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
IFT52	Strong	Autosomal recessive	short-rib thoracic dysplasia 16 with or without polydactyly	6

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
IFT52	Orphanet:1515	Cranioectodermal dysplasia

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
IFT52	HGNC:15901	ENSG00000101052	Q9Y366	Intraflagellar transport protein 52 homolog	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
IFT52	Intraflagellar transport protein 52 homolog	Involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia.

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)
IFT52	Other/Unknown	no		IFT52, Itf52_C, IFT52_GIFT

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
ganglionic eminence	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
IFT52	254	ubiquitous	marker	ganglionic eminence, cortical plate, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
IFT52	1,254

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
IFT52	Q9Y366	84.21

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
Intraflagellar transport	1	200.3×	0.006	IFT52
Hedgehog ‘off’ state	1	178.4×	0.006	IFT52

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
neural tube formation	1	2106.5×	0.004	IFT52
regulation of protein processing	1	1532.0×	0.004	IFT52
intraciliary anterograde transport	1	887.0×	0.004	IFT52
negative regulation of keratinocyte proliferation	1	702.2×	0.004	IFT52
keratinocyte proliferation	1	581.1×	0.004	IFT52
intraciliary transport	1	561.7×	0.004	IFT52
dorsal/ventral pattern formation	1	421.3×	0.004	IFT52
embryonic digit morphogenesis	1	300.9×	0.004	IFT52
non-motile cilium assembly	1	290.6×	0.004	IFT52
heart looping	1	267.5×	0.004	IFT52
smoothened signaling pathway	1	181.2×	0.006	IFT52
cilium assembly	1	73.6×	0.014	IFT52

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
IFT52	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	IFT52

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)
IFT52	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: IFT52