IFT52

Summary

IFT52 (intraflagellar transport 52, HGNC:15901) is a protein-coding gene on chromosome 20q13.12, encoding Intraflagellar transport protein 52 homolog (Q9Y366). 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.

This gene encodes a conserved proline-rich protein that is a component of the intraflagellar transport-B (IFT-B) core complex. The encoded protein is essential for the integrity of the IFT-B core complex, and for biosynthesis and maintenance of cilia. Mutations in this gene are associated with ciliopathy that affects the skeleton.

Source: NCBI Gene 51098 — RefSeq curated summary.

At a glance

• Gene–disease (curated): short-rib thoracic dysplasia 16 with or without polydactyly (Strong, GenCC) — +1 more curated relationship
• GWAS associations: 1
• Clinical variants (ClinVar): 247 total — 5 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 59
• MANE Select transcript: NM_016004

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15901
Approved symbol	IFT52
Name	intraflagellar transport 52
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	CGI-53, NGD5, dJ1028D15.1, NGD2
Ensembl gene	ENSG00000101052
Ensembl biotype	protein_coding
OMIM	617094
Entrez	51098

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 20 protein_coding, 7 protein_coding_CDS_not_defined

ENST00000373030, ENST00000373039, ENST00000460014, ENST00000461012, ENST00000467024, ENST00000468420, ENST00000471199, ENST00000476986, ENST00000486243, ENST00000871354, ENST00000871355, ENST00000871356, ENST00000871357, ENST00000871358, ENST00000871359, ENST00000871360, ENST00000932897, ENST00000932898, ENST00000932899, ENST00000932900, ENST00000932901, ENST00000932902, ENST00000932903, ENST00000970673, ENST00000970674, ENST00000970675, ENST00000970676

RefSeq mRNA: 7 — MANE Select: NM_016004 NM_001303458, NM_001303459, NM_001323578, NM_001323579, NM_001323580, NM_001323581, NM_016004

CCDS: CCDS33470

Canonical transcript exons

ENST00000373030 — 14 exons

Exon	Start	End
ENSE00000662190	43603760	43603889
ENSE00001459431	43594693	43594817
ENSE00001459434	43590937	43591054
ENSE00001640061	43642479	43642624
ENSE00001654556	43637145	43637253
ENSE00001886394	43646936	43647299
ENSE00003508505	43613850	43613976
ENSE00003524919	43596435	43596522
ENSE00003551828	43620857	43620925
ENSE00003610475	43623891	43624045
ENSE00003615662	43618940	43619026
ENSE00003659300	43605002	43605073
ENSE00003688849	43635926	43636013
ENSE00003694077	43604183	43604258

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 94.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 26.3213 / max 393.6424, expressed in 1808 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184670	26.3213	1808

Top tissues by expression

276 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	94.53	gold quality
cortical plate	UBERON:0005343	94.19	gold quality
ventricular zone	UBERON:0003053	93.43	gold quality
right uterine tube	UBERON:0001302	93.19	gold quality
bronchial epithelial cell	CL:0002328	93.13	gold quality
epithelium of bronchus	UBERON:0002031	92.63	gold quality
left ovary	UBERON:0002119	92.40	gold quality
bronchus	UBERON:0002185	92.16	gold quality
right ovary	UBERON:0002118	92.03	gold quality
embryo	UBERON:0000922	91.98	gold quality
right testis	UBERON:0004534	91.97	gold quality
endocervix	UBERON:0000458	91.96	gold quality
left testis	UBERON:0004533	91.96	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.46	gold quality
tibial artery	UBERON:0007610	91.23	gold quality
popliteal artery	UBERON:0002250	91.22	gold quality
adrenal tissue	UBERON:0018303	91.18	gold quality
testis	UBERON:0000473	91.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.12	gold quality
ovary	UBERON:0000992	91.02	gold quality
ectocervix	UBERON:0012249	90.67	gold quality
right coronary artery	UBERON:0001625	90.56	gold quality
body of uterus	UBERON:0009853	90.50	gold quality
aorta	UBERON:0000947	90.40	gold quality
gall bladder	UBERON:0002110	90.38	gold quality
stromal cell of endometrium	CL:0002255	90.31	gold quality
mucosa of stomach	UBERON:0001199	89.51	gold quality
left uterine tube	UBERON:0001303	89.49	gold quality
tibial nerve	UBERON:0001323	89.46	gold quality
descending thoracic aorta	UBERON:0002345	89.46	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.66
E-MTAB-6058	no	245.79
E-MTAB-7249	no	193.24

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting IFT52, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-10399-5P	99.17	69.87	2610
HSA-MIR-6504-3P	99.17	69.31	2891
HSA-MIR-1843	98.97	66.07	838
HSA-MIR-4802-5P	98.97	66.26	833
HSA-MIR-3161	98.71	67.14	816
HSA-MIR-496	98.66	69.80	931
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-6830-3P	98.62	68.07	1760
HSA-MIR-541-5P	98.24	67.77	1181
HSA-MIR-3144-3P	98.15	67.34	677
HSA-MIR-4432	97.80	67.87	705
HSA-MIR-3200-5P	97.34	65.97	826

Literature-anchored findings (GeneRIF, showing 7)

• Whole-exome sequencing revealed a homozygous nonsense variant p.R142* in IFT52 encoding an IFT-B core complex protein as the probable cause of her condition. This is the first report of a human disease associated with IFT52 (PMID:26880018)
• The data identify a new locus for short-rib polydactyly syndromes (SRPS) and show that IFT52 mutations result in a ciliopathy with primary effects on the skeleton. (PMID:27466190)
• This report expands ocular phenotypes of IFT52 mutation-caused ciliopathy to include retinal ciliopathy and demonstrates its deleterious nature in interrupting primary ciliary function. (PMID:30242358)
• our data allowed to have a better comprehensive overview of the genotype/phenotype correlation associated to IFT52 mutations and shed light on a novel function of IFT52 on centriole cohesion via the regulation of microtubule anchorage and dynamics. (PMID:31042281)
• Molecular basis underlying the ciliary defects caused by IFT52 variations found in skeletal ciliopathies. (PMID:35704471)
• The intraflagellar transport protein IFT52 associated with short-rib thoracic dysplasia is essential for ciliary function in osteogenic differentiation in vitro and for sensory perception in Drosophila. (PMID:35839863)
• The emerging functions of intraflagellar transport 52 in ciliary transport and ciliopathies. (PMID:38272449)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ift52	ENSDARG00000045025
mus_musculus	Ift52	ENSMUSG00000017858
rattus_norvegicus	Ift52	ENSRNOG00000007692
drosophila_melanogaster	IFT52	FBGN0031829
caenorhabditis_elegans		WBGENE00003886

Protein

Protein identifiers

Intraflagellar transport protein 52 homolog — Q9Y366 (reviewed: Q9Y366)

Alternative names: Protein NGD5 homolog

All UniProt accessions (1): Q9Y366

UniProt curated annotations — full annotation on UniProt →

Function. 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. Required for the anterograde transport of IFT88.

Subunit / interactions. Component of the IFT complex B, at least composed of IFT20, IFT22, IFT25, IFT27, IFT46, IFT52, TRAF3IP1/IFT54, IFT57, IFT74, IFT80, IFT81, and IFT88. Interacts with IFT88. Interacts with TTC25. Interacts with TTC21A. Interacts with IFT70A1, IFT70A2, IFT70B and KIF17. Interacts with USH1G.

Subcellular location. Cell projection. Cilium.

Disease relevance. Short-rib thoracic dysplasia 16 with or without polydactyly (SRTD16) [MIM:617102] A form of short-rib thoracic dysplasia, a group of autosomal recessive ciliopathies that are characterized by a constricted thoracic cage, short ribs, shortened tubular bones, and a ’trident’ appearance of the acetabular roof. Polydactyly is variably present. Non-skeletal involvement can include cleft lip/palate as well as anomalies of major organs such as the brain, eye, heart, kidneys, liver, pancreas, intestines, and genitalia. Some forms of the disease are lethal in the neonatal period due to respiratory insufficiency secondary to a severely restricted thoracic cage, whereas others are compatible with life. Disease spectrum encompasses Ellis-van Creveld syndrome, asphyxiating thoracic dystrophy (Jeune syndrome), Mainzer-Saldino syndrome, and short rib-polydactyly syndrome. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (7): NP_001290387, NP_001290388, NP_001310507, NP_001310508, NP_001310509, NP_001310510, NP_057088* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039975	IFT52	Family
IPR048643	Itf52_C	Domain
IPR055458	IFT52_GIFT	Domain
IPR055460	IFT52_central	Domain

Pfam: PF21178, PF23352, PF23355

UniProt features (5 total): sequence conflict 3, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y366-F1	84.21	0.43

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-5610787	Hedgehog ‘off’ state
R-HSA-5620924	Intraflagellar transport

MSigDB gene sets: 311 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_UP, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_CELL_PROLIFERATION, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, AREB6_01, GOBP_NEURAL_TUBE_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_EMBRYONIC_EPITHELIUM, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_DORSAL_VENTRAL_PATTERN_FORMATION, GOBP_SPECIFICATION_OF_SYMMETRY, GOBP_ANIMAL_ORGAN_MORPHOGENESIS

GO Biological Process (14): neural tube formation (GO:0001841), heart looping (GO:0001947), smoothened signaling pathway (GO:0007224), dorsal/ventral pattern formation (GO:0009953), negative regulation of keratinocyte proliferation (GO:0010839), intraciliary anterograde transport (GO:0035720), intraciliary transport (GO:0042073), embryonic digit morphogenesis (GO:0042733), keratinocyte proliferation (GO:0043616), cilium assembly (GO:0060271), regulation of protein processing (GO:0070613), non-motile cilium assembly (GO:1905515), determination of left/right symmetry (GO:0007368), cell projection organization (GO:0030030)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (13): centrosome (GO:0005813), centriole (GO:0005814), cilium (GO:0005929), intraciliary transport particle A (GO:0030991), intraciliary transport particle B (GO:0030992), motile cilium (GO:0031514), photoreceptor connecting cilium (GO:0032391), ciliary basal body (GO:0036064), dendrite terminus (GO:0044292), ciliary tip (GO:0097542), ciliary base (GO:0097546), cell projection (GO:0042995), photoreceptor cell cilium (GO:0097733)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Signaling by Hedgehog	1
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cilium	5
cellular anatomical structure	4
microtubule organizing center	3
intraciliary transport particle	3
cilium organization	2
protein-containing complex	2
ciliary transition zone	2
embryonic epithelial tube formation	1
neural tube development	1
embryonic heart tube morphogenesis	1
determination of heart left/right asymmetry	1
cell surface receptor signaling pathway	1
regionalization	1
regulation of keratinocyte proliferation	1
keratinocyte proliferation	1
negative regulation of epithelial cell proliferation	1
intraciliary transport	1
transport along microtubule	1
embryonic limb morphogenesis	1
embryonic morphogenesis	1
epithelial cell proliferation	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
protein processing	1
regulation of proteolysis	1
regulation of protein maturation	1
cilium assembly	1
determination of bilateral symmetry	1
left/right pattern formation	1
cellular component organization	1
binding	1
centriole	1
intracellular membraneless organelle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

1118 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IFT52	IFT46	Q9NQC8	997
IFT52	IFT57	Q9NWB7	997
IFT52	IFT88	Q13099	997
IFT52	IFT70B	Q8N4P2	997
IFT52	IFT27	Q9BW83	996
IFT52	IFT74	Q96LB3	995
IFT52	IFT81	Q8WYA0	993
IFT52	IFT25	Q9Y547	990
IFT52	IFT22	Q9H7X7	989
IFT52	IFT20	Q8IY31	986
IFT52	IFT80	Q9P2H3	982
IFT52	IFT38	Q96AJ1	980
IFT52	IFT172	Q9UG01	971
IFT52	IFT54	Q8TDR0	962
IFT52	IFT140	Q96RY7	903

IntAct

79 interactions, top by confidence:

A	B	Type	Score
IFT56	IFT70A	psi-mi:“MI:0914”(association)	0.790
IFT70A	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT70B	IFT56	psi-mi:“MI:0914”(association)	0.790
IFT25	IFT56	psi-mi:“MI:0914”(association)	0.690
IFT27	IFT56	psi-mi:“MI:0914”(association)	0.690
RHPN1	PODXL	psi-mi:“MI:0914”(association)	0.690
IFT22	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT46	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT88	IFT56	psi-mi:“MI:0914”(association)	0.640
IFT57	IFT56	psi-mi:“MI:0914”(association)	0.640

BioGRID (57): IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Co-fractionation), UBXN10 (Reconstituted Complex), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS), IFT52 (Affinity Capture-MS)

ESM2 similar proteins: A2X0Q3, A7YW45, A8BQB4, F4JWP9, O14744, O42130, O42131, O46374, O80585, P11388, P35573, P35574, P41515, P45437, Q01320, Q02880, Q08DS5, Q295E6, Q29G21, Q4R5M3, Q5BLF0, Q5R698, Q5RC82, Q62559, Q62991, Q64399, Q64511, Q6ESI7, Q6GNS3, Q6NUA1, Q6P2Z6, Q6YXZ7, Q75HE6, Q7QJW7, Q803R5, Q8AVL0, Q8BRF7, Q8CIG8, Q8GWT4, Q8K224

Diamond homologs: Q62559, Q9Y366

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 49 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Intraflagellar transport	14	85.0×	2e-22
Cilium Assembly	5	16.5×	1e-03
Organelle biogenesis and maintenance	5	10.0×	1e-02

GO biological processes:

GO term	Partners	Fold	FDR
intraciliary anterograde transport	13	262.1×	4e-28
intraciliary transport	9	114.9×	7e-15
non-motile cilium assembly	7	46.2×	1e-08
smoothened signaling pathway	9	37.1×	2e-10
cilium assembly	14	23.4×	6e-14

Disease & clinical

Clinical variants and AI predictions

ClinVar

247 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	1
Uncertain significance	88
Likely benign	101
Benign	30

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
253306	NM_016004.5(IFT52):c.424C>T (p.Arg142Ter)	Pathogenic
964973	NM_016004.5(IFT52):c.820C>T (p.Arg274Ter)	Pathogenic
983487	NM_016004.5(IFT52):c.695_699delinsCA (p.Ile232_Met233delinsThr)	Pathogenic
983488	NM_016004.5(IFT52):c.556A>G (p.Thr186Ala)	Pathogenic
983489	NM_016004.5(IFT52):c.293A>G (p.Asn98Ser)	Pathogenic
253307	NM_016004.5(IFT52):c.595G>A (p.Ala199Thr)	Likely pathogenic

SpliceAI

1694 predictions. Top by Δscore:

Variant	Effect	Δscore
20:43594688:A:AG	acceptor_gain	1.0000
20:43594688:ATAAG:A	acceptor_gain	1.0000
20:43594689:T:G	acceptor_gain	1.0000
20:43594690:A:AG	acceptor_gain	1.0000
20:43594690:AAG:A	acceptor_gain	1.0000
20:43594691:A:G	acceptor_gain	1.0000
20:43594692:G:A	acceptor_gain	1.0000
20:43594692:G:GG	acceptor_gain	1.0000
20:43594692:GGT:G	acceptor_gain	1.0000
20:43594692:GGTA:G	acceptor_gain	1.0000
20:43594692:GGTAA:G	acceptor_gain	1.0000
20:43594806:G:GT	donor_gain	1.0000
20:43594814:AGAG:A	donor_loss	1.0000
20:43594815:GAG:G	donor_gain	1.0000
20:43594816:AGG:A	donor_loss	1.0000
20:43594817:GGTGA:G	donor_loss	1.0000
20:43594818:G:GA	donor_loss	1.0000
20:43594819:T:G	donor_loss	1.0000
20:43603755:TGTAG:T	acceptor_loss	1.0000
20:43603756:GTA:G	acceptor_loss	1.0000
20:43603757:TA:T	acceptor_loss	1.0000
20:43603758:A:AG	acceptor_gain	1.0000
20:43603758:AGTT:A	acceptor_loss	1.0000
20:43603758:AGTTT:A	acceptor_gain	1.0000
20:43603759:G:GG	acceptor_gain	1.0000
20:43603759:GT:G	acceptor_gain	1.0000
20:43603759:GTT:G	acceptor_gain	1.0000
20:43603759:GTTT:G	acceptor_gain	1.0000
20:43603759:GTTTG:G	acceptor_gain	1.0000
20:43603889:GGTA:G	donor_loss	1.0000

AlphaMissense

2921 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:43613960:C:A	A199D	0.998
20:43619014:C:A	N229K	0.998
20:43619014:C:G	N229K	0.998
20:43613912:T:A	V183D	0.997
20:43613959:G:C	A199P	0.997
20:43596481:T:A	W56R	0.996
20:43596481:T:C	W56R	0.996
20:43604256:C:A	N137K	0.996
20:43604256:C:G	N137K	0.996
20:43613903:C:A	A180E	0.996
20:43618962:T:A	V212E	0.995
20:43642612:G:C	K418N	0.995
20:43642612:G:T	K418N	0.995
20:43613902:G:C	A180P	0.993
20:43613915:T:C	L184P	0.993
20:43618956:T:C	L210P	0.993
20:43620876:T:C	L240P	0.993
20:43642607:T:C	F417L	0.993
20:43642609:C:A	F417L	0.993
20:43642609:C:G	F417L	0.993
20:43596509:T:C	F65S	0.992
20:43613891:T:A	V176D	0.992
20:43618968:G:A	G214D	0.992
20:43620872:T:A	W239R	0.992
20:43620872:T:C	W239R	0.992
20:43594793:T:C	L32P	0.991
20:43618970:T:C	S215P	0.991
20:43596479:T:C	L55P	0.990
20:43603806:T:A	V85E	0.990
20:43603852:C:A	N100K	0.990

dbSNP variants (sampled 300 via entrez): RS1000068752 (20:43626576 T>C), RS1000087290 (20:43602730 G>A), RS1000139507 (20:43602502 T>G), RS1000153660 (20:43646585 A>G,T), RS1000159194 (20:43627068 A>G), RS1000283751 (20:43590820 T>A), RS1000294472 (20:43627352 T>G), RS1000308951 (20:43633343 C>A,G), RS1000319303 (20:43639260 G>C), RS1000391797 (20:43647760 C>A), RS1000424279 (20:43602802 G>T), RS1000429997 (20:43610120 A>G), RS1000622644 (20:43591883 A>G,T), RS1000729144 (20:43608777 T>C), RS1000802616 (20:43615986 A>G)

Disease associations

OMIM: gene MIM:617094 | disease phenotypes: MIM:617102, MIM:208500

GenCC curated gene-disease

Disease	Classification	Inheritance
short-rib thoracic dysplasia 16 with or without polydactyly	Strong	Autosomal recessive
cranioectodermal dysplasia	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
short-rib thoracic dysplasia 16 with or without polydactyly	Moderate	AR

Mondo (4): short-rib thoracic dysplasia 16 with or without polydactyly (MONDO:0014915), short rib-polydactyly syndrome (MONDO:0015461), Jeune syndrome (MONDO:0018770), cranioectodermal dysplasia (MONDO:0009032)

Orphanet (2): Short rib-polydactyly syndrome (Orphanet:1505), Jeune syndrome (Orphanet:474)

HPO phenotypes

59 total (30 of 59 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000164	Abnormality of the dentition
HP:0000232	Everted lower lip vermilion
HP:0000268	Dolichocephaly
HP:0000269	Prominent occiput
HP:0000286	Epicanthus
HP:0000293	Full cheeks
HP:0000348	High forehead
HP:0000369	Low-set ears
HP:0000431	Wide nasal bridge
HP:0000463	Anteverted nares
HP:0000506	Telecanthus
HP:0000540	Hypermetropia
HP:0000545	Myopia
HP:0000601	Hypotelorism
HP:0000639	Nystagmus
HP:0000668	Hypodontia
HP:0000670	Carious teeth
HP:0000679	Taurodontia
HP:0000682	Abnormal dental enamel morphology
HP:0000687	Widely spaced teeth
HP:0000691	Microdontia
HP:0000767	Pectus excavatum
HP:0000774	Narrow chest
HP:0000939	Osteoporosis
HP:0000940	Abnormal diaphysis morphology
HP:0000944	Abnormal metaphysis morphology
HP:0001156	Brachydactyly
HP:0001231	Abnormal fingernail morphology
HP:0001270	Motor delay

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002396_57	Mean reticulocyte volume	7.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010701	mean reticulocyte volume

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D012779	Short Rib-Polydactyly Syndrome	C05.116.099.708.857; C05.660.585.600.750; C16.131.077.850; C16.131.621.585.600.750
C537571	Jeune syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tobacco Smoke Pollution	decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
pirinixic acid	decreases expression, increases activity, affects binding	1
bisphenol A	affects cotreatment, increases methylation	1
trichostatin A	affects expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Air Pollutants, Occupational	affects expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Doxorubicin	decreases expression	1
Estradiol	affects expression	1
Hydrogen Peroxide	increases expression	1
Methyl Methanesulfonate	increases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

6 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04032756	Not specified	TERMINATED	Tofacitinib Registry of Patients With Ulcerative Colitis in Germany
NCT04184531	Not specified	UNKNOWN	Sensenbrenner Clinical Study
NCT06626282	Not specified	RECRUITING	Fertility and Ovarian Reserve in Female Childhood Cancer Survivors
NCT00948376	Not specified	COMPLETED	Natural History of Asphyxiating Thoracic Dystrophy (DTJ)
NCT04143841	Not specified	TERMINATED	Viveye Ocular Magnetic Neurostimulation System (OMNS) for the Management of Severe Dry Eye Disease
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)