INTU

protein-coding

inturned 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]

Previous symbols:
  • PDZK6
  • PDZD6

MANE transcript

NM_015693.4

Inheritance

AR

ClinVar variants

P:12U:276B:93

Top phenotype

Orofaciodigital syndrome XVII; Short-rib thoracic dysplasia 20 with polydactyly

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr4:127,623,271-127,726,737

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~103.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

orofaciodigital syndrome 17LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0033375

Submitter: Labcorp Genetics (formerly Invitae)

INTU-related skeletal ciliopathyDEFINITIVE

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).

short-rib thoracic dysplasia 20 with polydactylyLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0044328

Submitter: Labcorp Genetics (formerly Invitae)

orofaciodigital syndrome 17MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0033375

Submitter: Ambry Genetics

orofaciodigital syndrome 17STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033375

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Orofaciodigital syndrome XVII; Short-rib thoracic dysplasia 20 with polydactylyAR

Manifestation: Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Pulmonary

Intervention: Cardiovascular

Rationale: The condition can involve congenital cardiac anomalies, and awareness may allow early management

Refs: 27158779Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to INTU variants in ClinVar

14 Conditions Cataloged
not providedTotal: 360
Inborn genetic diseasesTotal: 110
INTU-related disorderTotal: 22
not specifiedTotal: 13
Orofaciodigital syndrome 17Total: 9
Short-rib thoracic dysplasia 20 with polydactylyTotal: 9
Short rib-polydactyly syndromeTotal: 2
Jeune thoracic dystrophyTotal: 2

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
71
clinvar
1
clinvar
74
missense
2
clinvar
254
clinvar
14
clinvar
7
clinvar
277
nonsense
4
clinvar
9
clinvar
13
start loss
0
frameshift
2
clinvar
4
clinvar
7
clinvar
13
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total210276858381

Highest pathogenic variant AF is 0.00008551288

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015693.4RefSeqNP_056508.216MANE Select
ENST00000335251.11EnsemblENSP00000334003.516MANE Select
ENST00000503626.5EnsemblENSP00000426287.17Standard
ENST00000503952.5EnsemblENSP00000421995.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.3844634870.9510.00002456144
Missense (PolyPhen)103118.170.871651601
Synonymous1.171591790.8890.000009181816
Loss of Function2.912242.50.5180.00000197567

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000870.00062rare
Latino/Admixed American0.000330.00032rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000330.00033rare
Finnish00.0absent
European (Non-Finnish)0.000410.00041rare
South Asian0.000230.00023rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.