INTU
protein-codinginturned planar cell polarity protein, the group of Ciliogenesis and planar polarity effector complex subunits|PDZ domain containing
Gene summary
Predicted to enable phosphatidylinositol binding activity. Involved in embryonic digit morphogenesis; roof of mouth development; and tongue morphogenesis. Located in ciliary basal body and motile cilium. Implicated in asphyxiating thoracic dystrophy and orofaciodigital syndrome XVII. [provided by Alliance of Genome Resources, Jun 2026]
- PDZK6
- PDZD6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~103.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0033375
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:1060154
Submitter: ClinGen
*INTU* was first reported in relation to autosomal recessive *INTU*-related skeletal ciliopathy in 2016 (Toriyama et al. 2016, PMID: 27158779). *INTU*-related skeletal ciliopathy is characterized by facial dysmorphism, tongue nodules, developmental delay, and polydactyly, as well as other syndromic findings. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in molecular mechanism, inheritance pattern, or phenotypic variability between orofaciodigital syndrome XVII (MIM: 617926) and short-rib thoracic dysplasia 20 with polydactyly (MIM: 617925). Therefore, the two disease assertions have been lumped into one entity, *INTU*-related skeletal ciliopathy. A total of 2 missense, 2 frameshift, 1 nonsense, and 1 CNV that have been reported in four probands in three publications (PMIDs: 27158779, 29451301, 34623732) are included in this curation. The mechanism of pathogenicity at this time is unknown. This gene-disease relationship is also supported by two mouse models, rescue in non-human model organisms, biochemical function studies, and protein-protein interactions (PMIDs: 20067783, 22935613, 25774014, 27158779). In summary, there is definitive evidence supporting the relationship between *INTU* and autosomal recessive *INTU*-related skeletal ciliopathy. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.This classification was approved by the ClinGen Skeletal Disorders GCEP on the meeting date June 2nd, 2025 (SOP Version 11).
Inheritance Pattern: Unknown
Disease ID:MONDO:0044328
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0033375
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0033375
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Pulmonary
Intervention: Cardiovascular
Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to INTU variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015693.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 71 | 1 | 74 | ||
| missense | 2 | 254 | 14 | 7 | 277 | |
| nonsense | 4 | 9 | 13 | |||
| start loss | 0 | |||||
| frameshift | 2 | 4 | 7 | 13 | ||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 2 | 10 | 276 | 85 | 8 | 381 |
Highest pathogenic variant AF is 0.00008551288
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056508.2 | 16 | MANE Select | |
| Ensembl | ENSP00000334003.5 | 16 | MANE Select | |
| Ensembl | ENSP00000426287.1 | 7 | Standard | |
| Ensembl | ENSP00000421995.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- establishment of planar polarity
- nervous system development
- regulation of smoothened signaling pathway
- negative regulation of keratinocyte proliferation
- spinal cord dorsal/ventral patterning
Molecular Function
- protein binding
Cellular Component
- cytoplasm
- cell surface
- motile cilium
- ciliary basal body
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335251
- Coding exons
- 16
- Length
- 103467
- Individuals with no LoFs
- 125663
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 84
- Defined
- 125747
- p
- 0.000334
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.384 | 463 | 487 | 0.951 | 0.0000245 | 6144 |
| Missense (PolyPhen) | 103 | 118.17 | 0.87165 | 1601 | ||
| Synonymous | 1.17 | 159 | 179 | 0.889 | 0.00000918 | 1816 |
| Loss of Function | 2.91 | 22 | 42.5 | 0.518 | 0.00000197 | 567 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00087 | 0.00062 | rare |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00041 | 0.00041 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a key role in ciliogenesis and embryonic development. Regulator of cilia formation by controlling the organization of the apical actin cytoskeleton and the positioning of the basal bodies at the apical cell surface, which in turn is essential for the normal orientation of elongating ciliary microtubules. Plays a key role in definition of cell polarity via its role in ciliogenesis but not via conversion extension. Has an indirect effect on hedgehog signaling (By similarity). Proposed to function as core component of the CPLANE (ciliogenesis and planar polarity effectors) complex involved in the recruitment of peripheral IFT-A proteins to basal bodies (PubMed:27158779). {ECO:0000250|UniProtKB:Q059U7, ECO:0000250|UniProtKB:Q2I0E5, ECO:0000305|PubMed:27158779}.;
- Disease
- DISEASE: Short-rib thoracic dysplasia 20 with polydactyly (SRTD20) [MIM:617925]: 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. {ECO:0000269|PubMed:27158779}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Orofaciodigital syndrome 17 (OFD17) [MIM:617926]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD17 inheritance is autosomal recessive. {ECO:0000269|PubMed:27158779}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Short-rib thoracic dysplasia 7/20 with polydactyly, digenic (SRTD7/20) [MIM:614091]: A digenic form of short-rib thoracic dysplasia caused by double heterozygosity for a mutation in the WDR35 gene and a mutation in the INTU gene. Short-rib thoracic dysplasia is part of a group of 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. Note=The disease is caused by mutations affecting distinct genetic loci, including the gene represented in this entry. SRTD7/20 can be caused by co-occurrence of WDR35 variant p.Trp311Leu and INTU p.Gln276Ter. One such patient has been reported. {ECO:0000269|PubMed:27158779}.;
Recessive Scores
- pRec
- 0.223
Intolerance Scores
- LoFtool
- 0.189
- RVIS EVS
- -0.53
- RVIS percentile EVS
- 20.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.177
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |