Isolated cleft palate

disease
On this page

Also known as cleft palate, isolatedCPIdominant cleft palatenonsyndromic cleft palate

Summary

Isolated cleft palate (MONDO:0007336) is a disease with 10 cohort genes.

At a glance

  • Cohort genes: 10
  • ClinVar variants: 13

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameisolated cleft palate
Mondo IDMONDO:0007336
OMIM119540
DOIDDOID:0110213
UMLSC1837218
MedGen332392
GARD0001896
Is cancer (heuristic)no

Also known as: cleft palate, isolated · CPI · dominant cleft palate · isolated cleft palate · nonsyndromic cleft palate

Data availability: 13 ClinVar variants · 7 GenCC gene-disease records.

Disease family

An umbrella term covering 1 Mondo subtype.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseaseorofacial cleftcleft palateisolated cleft palate

Related subtypes (8): cleft soft palate, Rapp-Hodgkin syndrome, bifid uvula, cleft palate with or without ankyloglossia, X-linked, cleft hard palate, submucosal cleft palate, Kuster syndrome, soft and hard cleft palate

Subtypes (1): orofacial cleft 3

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

13 retrieved; paginated sample, class counts are floors:

5 pathogenic, 3 conflicting classifications of pathogenicity, 2 uncertain significance, 1 likely pathogenic, 1 benign/likely benign, 1 benign

ClinVarVariant (HGVS)GeneClassificationReview
1172586NM_198173.3(GRHL3):c.1172G>A (p.Arg391His)GRHL3Pathogenicno assertion criteria provided
219244NM_198173.3(GRHL3):c.840+1G>TGRHL3Pathogeniccriteria provided, single submitter
219245NM_198173.3(GRHL3):c.916dup (p.Arg306fs)GRHL3Pathogeniccriteria provided, single submitter
219246NM_198173.3(GRHL3):c.1285+2delGRHL3Pathogeniccriteria provided, single submitter
522269NM_001172509.2(SATB2):c.1375C>T (p.Arg459Ter)SATB2Pathogeniccriteria provided, multiple submitters, no conflicts
1172584NM_198173.3(GRHL3):c.22A>G (p.Arg8Gly)GRHL3Likely pathogenicno assertion criteria provided
219243NM_198173.3(GRHL3):c.738C>T (p.Gly246=)GRHL3Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
39617NM_006206.6(PDGFRA):c.1631T>C (p.Val544Ala)PDGFRAConflicting classifications of pathogenicitycriteria provided, conflicting classifications
39618NM_006206.6(PDGFRA):c.3155C>T (p.Thr1052Met)PDGFRAConflicting classifications of pathogenicitycriteria provided, conflicting classifications
1338788NM_004815.4(ARHGAP29):c.1865C>T (p.Thr622Met)ARHGAP29Uncertain significancecriteria provided, single submitter
1172585NM_198173.3(GRHL3):c.32G>A (p.Arg11Gln)GRHL3Uncertain significancecriteria provided, single submitter
697696NM_198173.3(GRHL3):c.800C>G (p.Ala267Gly)GRHL3Benigncriteria provided, multiple submitters, no conflicts
39616NM_006206.6(PDGFRA):c.1202C>A (p.Ala401Asp)PDGFRABenign/Likely benigncriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 18 · Orphanet: 20 · 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.

GeneClassificationInheritanceDiseaseRecords
ACACBLimitedUnknownisolated cleft palate
DENND4BLimitedUnknownisolated cleft palate
PDGFRALimitedUnknownisolated cleft palate8
ARID5BNo Known Disease RelationshipUnknownisolated cleft palate
MIB1No Known Disease RelationshipUnknownisolated cleft palate5
MORN5No Known Disease RelationshipUnknownisolated cleft palate
UBBNo Known Disease RelationshipAutosomal dominantisolated cleft palate

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
PDGFRAOrphanet:168940Chronic eosinophilic leukemia
PDGFRAOrphanet:168947Myeloid/lymphoid neoplasm associated with PDGFRA rearrangement
PDGFRAOrphanet:199306Cleft lip/palate
PDGFRAOrphanet:314950Primary hypereosinophilic syndrome
PDGFRAOrphanet:44890Gastrointestinal stromal tumor
PDGFRAOrphanet:585877B-lymphoblastic leukemia/lymphoma with recurrent genetic abnormality
UBBOrphanet:101023Cleft hard palate
UBBOrphanet:155878Submucosal cleft palate
UBBOrphanet:99771Bifid uvula
UBBOrphanet:99772Cleft velum
MIB1Orphanet:54260Left ventricular noncompaction
SATB2Orphanet:2510192q32q33 deletion syndrome
SATB2Orphanet:251028SATB2-associated syndrome due to a chromosomal rearrangement
SATB2Orphanet:576283SATB2-associated syndrome due to a pathogenic variant
GRHL3Orphanet:101023Cleft hard palate
GRHL3Orphanet:155878Submucosal cleft palate
GRHL3Orphanet:888Van der Woude syndrome
GRHL3Orphanet:99771Bifid uvula
GRHL3Orphanet:99772Cleft velum
ARHGAP29Orphanet:199306Cleft lip/palate

Cohort genes → proteins

10 cohort genes, 10 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence10

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
PDGFRAHGNC:8803ENSG00000134853P16234Platelet-derived growth factor receptor alphagencc,clinvar
UBBHGNC:12463ENSG00000170315P0CG47Polyubiquitin-Bgencc
ARID5BHGNC:17362ENSG00000150347Q14865AT-rich interactive domain-containing protein 5Bgencc
MORN5HGNC:17841ENSG00000185681Q5VZ52MORN repeat-containing protein 5gencc
MIB1HGNC:21086ENSG00000101752Q86YT6E3 ubiquitin-protein ligase MIB1gencc
DENND4BHGNC:29044ENSG00000198837O75064DENN domain-containing protein 4Bgencc
ACACBHGNC:85ENSG00000076555O00763Acetyl-CoA carboxylase 2gencc
SATB2HGNC:21637ENSG00000119042Q9UPW6DNA-binding protein SATB2clinvar
GRHL3HGNC:25839ENSG00000158055Q8TE85Grainyhead-like protein 3 homologclinvar
ARHGAP29HGNC:30207ENSG00000137962Q52LW3Rho GTPase-activating protein 29clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
PDGFRAPlatelet-derived growth factor receptor alphaTyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis.
UBBPolyubiquitin-BExists either covalently attached to another protein, or free (unanchored).
ARID5BAT-rich interactive domain-containing protein 5BTranscription coactivator that binds to the 5’-AATA[CT]-3’ core sequence and plays a key role in adipogenesis and liver development.
MIB1E3 ubiquitin-protein ligase MIB1E3 ubiquitin-protein ligase that mediates ubiquitination of Delta receptors, which act as ligands of Notch proteins.
DENND4BDENN domain-containing protein 4BGuanine nucleotide exchange factor (GEF) which may activate RAB10.
ACACBAcetyl-CoA carboxylase 2Mitochondrial enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA and plays a central role in fatty acid metabolism.
SATB2DNA-binding protein SATB2Binds to DNA, at nuclear matrix- or scaffold-associated regions.
GRHL3Grainyhead-like protein 3 homologTranscription factor playing important roles in primary neurulation and in the differentiation of stratified epithelia of both ectodermal and endodermal origin.
ARHGAP29Rho GTPase-activating protein 29GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state.

Protein-family classification

Druggable: 2 · Difficult: 4 · Unknown: 4 · Druggable fraction: 0.2

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.

FamilyGenesFoldFDR
Transcription factor32.5×0.555
Kinase12.8×0.727
Scaffold/PPI11.7×0.727
Enzyme (other)11.2×0.727
Other/Unknown40.7×0.907

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
PDGFRAKinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Tyr_kinase_rcpt_3_CS
UBBOther/UnknownnoUbiquitin-like_dom, Ubiquitin_CS, Ubiquitin_dom
ARID5BOther/UnknownnoARID_dom, ARID5B_ARID/BRIGHT_DNA-bd, ARID_dom_sf
MORN5Other/UnknownnoMORN, Morn5
MIB1Transcription factornoZnf_ZZ, Znf_RING, Ankyrin_rpt
DENND4BOther/UnknownnocDENN_dom, PPR_rpt, dDENN_dom
ACACBEnzyme (other)yes6.3.4.14Biotin_lipoyl, CPAse_ATP-bd, BC-like_N
SATB2Transcription factornoHD, CUT_dom, Homeodomain-like_sf
GRHL3Transcription factornoCP2, TF_CP2-like, GRHL1/CP2_C
ARHGAP29Scaffold/PPInoRhoGAP_dom, PKC_DAG/PE, Rho_GTPase_activation_prot

Expression context

Cohort genes with no expression data: 0.

10 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)10
unknown0

Top tissues across cohort

TissueCohort genes
tibia2
decidua1
synovial joint1
adult organism1
endothelial cell1
pons1
pericardium1
saphenous vein1
type B pancreatic cell1
bronchial epithelial cell1
bronchus1
right uterine tube1
corpus epididymis1
kidney epithelium1
granulocyte1
right hemisphere of cerebellum1
spleen1
adipose tissue1
subcutaneous adipose tissue1
tendon of biceps brachii1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
PDGFRA289ubiquitousmarkertibia, decidua, synovial joint
UBB305ubiquitousmarkerpons, adult organism, endothelial cell
ARID5B299ubiquitousmarkertype B pancreatic cell, saphenous vein, pericardium
MORN5159broadmarkerbronchial epithelial cell, right uterine tube, bronchus
MIB1262ubiquitousmarkercorpus epididymis, kidney epithelium, tibia
DENND4B289ubiquitousmarkergranulocyte, right hemisphere of cerebellum, spleen
ACACB288ubiquitousmarkertendon of biceps brachii, adipose tissue, subcutaneous adipose tissue
SATB2235ubiquitousmarkerperiodontal ligament, cortical plate, mucosa of sigmoid colon
GRHL3164broadmarkerlower esophagus mucosa, esophagus mucosa, gingival epithelium
ARHGAP29283ubiquitousmarkervisceral pleura, parietal pleura, pleura

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PDGFRA5,186
ACACB2,991
MIB12,280
SATB22,254
ARID5B1,778
ARHGAP291,278
GRHL31,270
UBB1,252
MORN5836
DENND4B629

Intra-cohort edges

ABSources
ARHGAP29GRHL3string_interaction

Structural data

PDB: 6 · AlphaFold-only: 4 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
UBBP0CG47287
PDGFRAP1623415
ACACBO0076311
MIB1Q86YT66
SATB2Q9UPW63
ARID5BQ148652

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MORN5Q5VZ5291.19
DENND4BO7506473.32
ARHGAP29Q52LW364.41
GRHL3Q8TE8561.27

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 259. Enrichment computed across 10 evidence-associated genes (8 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 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Constitutive Signaling by NOTCH1 HD Domain Mutants2190.3×0.012UBB, MIB1
NOTCH3 Activation and Transmission of Signal to the Nucleus2119.0×0.012UBB, MIB1
NOTCH2 Activation and Transmission of Signal to the Nucleus2109.8×0.012UBB, MIB1
Activated NOTCH1 Transmits Signal to the Nucleus289.2×0.014UBB, MIB1
Imatinib-resistant PDGFR mutants11427.5×0.016PDGFRA
Sunitinib-resistant PDGFR mutants11427.5×0.016PDGFRA
Regorafenib-resistant PDGFR mutants11427.5×0.016PDGFRA
Sorafenib-resistant PDGFR mutants11427.5×0.016PDGFRA
PDGFR mutants bind TKIs11427.5×0.016PDGFRA
Constitutive Signaling by NOTCH1 PEST Domain Mutants249.2×0.016UBB, MIB1
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants249.2×0.016UBB, MIB1
Maturation of protein E1356.9×0.049UBB
Assembly Of The HIV Virion1203.9×0.049UBB
Modulation by Mtb of host immune system1203.9×0.049UBB
FLT3 signaling by CBL mutants1203.9×0.049UBB
ChREBP activates metabolic gene expression1158.6×0.049ACACB
Signaling by NOTCH1 HD Domain Mutants in Cancer1158.6×0.049MIB1
Myoclonic epilepsy of Lafora1158.6×0.049UBB
PTK6 Regulates RTKs and Their Effectors AKT1 and DOK11158.6×0.049UBB
InlA-mediated entry of Listeria monocytogenes into host cells1158.6×0.049UBB
Prevention of phagosomal-lysosomal fusion1158.6×0.049UBB
Downregulation of ERBB4 signaling1142.8×0.049UBB
IRAK2 mediated activation of TAK1 complex1142.8×0.049UBB
Biotin transport and metabolism1129.8×0.049ACACB
Regulation of PTEN localization1129.8×0.049UBB
TICAM1,TRAF6-dependent induction of TAK1 complex1129.8×0.049UBB
Alpha-protein kinase 1 signaling pathway1129.8×0.049UBB
Regulation of BACH1 activity1129.8×0.049UBB
Josephin domain DUBs1119.0×0.049UBB

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
roof of mouth development382.6×7e-04PDGFRA, ARID5B, SATB2
fat pad development2374.5×7e-04UBB, ARID5B
female gonad development2178.3×0.002UBB, ARID5B
adrenal gland development2149.8×0.002PDGFRA, ARID5B
platelet-derived growth factor receptor signaling pathway2124.8×0.003PDGFRA, ARID5B
face morphogenesis2110.1×0.003PDGFRA, ARID5B
embryonic skeletal system morphogenesis287.1×0.004PDGFRA, SATB2
lactic acid secretion11872.4×0.007ACACB
intracellular aspartate homeostasis11872.4×0.007ACACB
energy homeostasis260.4×0.007UBB, ACACB
protein homotetramerization252.7×0.007UBB, ACACB
wound healing250.6×0.007PDGFRA, GRHL3
hypothalamus gonadotrophin-releasing hormone neuron development1936.2×0.008UBB
platelet-derived growth factor receptor-alpha signaling pathway1936.2×0.008PDGFRA
regulation of cardiac muscle hypertrophy in response to stress1936.2×0.008ACACB
malonyl-CoA biosynthetic process1936.2×0.008ACACB
regulation of actin cytoskeleton organization235.0×0.010PDGFRA, GRHL3
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway1624.1×0.011PDGFRA
metanephric glomerular capillary formation1624.1×0.011PDGFRA
negative regulation of fatty acid beta-oxidation1468.1×0.012ACACB
positive regulation of heart growth1468.1×0.012ACACB
regulation of mesenchymal stem cell differentiation1468.1×0.012PDGFRA
positive regulation of protein monoubiquitination1374.5×0.015UBB
tricarboxylic acid metabolic process1312.1×0.016ACACB
intracellular glutamate homeostasis1312.1×0.016ACACB
positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator1312.1×0.016UBB
acetyl-CoA metabolic process1267.5×0.017ACACB
regulation of Rab protein signal transduction1267.5×0.017DENND4B
neural tube formation1234.1×0.018MIB1
modification-dependent protein catabolic process1234.1×0.018UBB

Therapeutics

Drug target analysis

Approved (phase 4): 2 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 8

Druggability breadth: 4 of 10 evidence-associated genes (40%) 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.

SymbolExample approved molecule
PDGFRAPONATINIB
ACACBBEMPEDOIC ACID

Top cohort targets by molecule count

SymbolMoleculesMax phase
PDGFRA774
ACACB44
UBB00
ARID5B00
MORN500
MIB100
DENND4B00
SATB200
GRHL300
ARHGAP2900

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
PONATINIB4PDGFRA
FEDRATINIB4PDGFRA
TIVOZANIB4PDGFRA
LENVATINIB4PDGFRA
AXITINIB4PDGFRA
SORAFENIB4PDGFRA
IMATINIB MESYLATE4PDGFRA
INFIGRATINIB PHOSPHATE4PDGFRA
INFIGRATINIB4PDGFRA
REGORAFENIB4PDGFRA
CERITINIB4PDGFRA
VANDETANIB4PDGFRA
NILOTINIB4PDGFRA
BOSUTINIB4PDGFRA
NINTEDANIB ESYLATE4PDGFRA
PEXIDARTINIB4PDGFRA
AVAPRITINIB4PDGFRA
RIPRETINIB4PDGFRA
PAZOPANIB4PDGFRA
NINTEDANIB4PDGFRA
SUNITINIB4PDGFRA
DASATINIB4PDGFRA
ERLOTINIB4PDGFRA
QUIZARTINIB4PDGFRA
MIDOSTAURIN4PDGFRA
IMATINIB4PDGFRA
BEMPEDOIC ACID4ACACB
VATALANIB3PDGFRA
MASITINIB3PDGFRA
CRENOLANIB3PDGFRA

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
PDGFRA1,172Binding:1160, Functional:8, ADMET:4
ACACB81Binding:81
SATB26Binding:6
UBB1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PDGFRA2.7.10.1receptor protein-tyrosine kinase
ACACB6.3.4.14, 6.4.1.2biotin carboxylase, acetyl-CoA carboxylase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
PDGFRA1,172

Pharmacogenomics

Cohort genes with a PharmGKB record: 10; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

30 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.

CompoundMax phaseCohort target (bioactivity)
PONATINIB4PDGFRA
FEDRATINIB4PDGFRA
TIVOZANIB4PDGFRA
LENVATINIB4PDGFRA
AXITINIB4PDGFRA
SORAFENIB4PDGFRA
IMATINIB MESYLATE4PDGFRA
INFIGRATINIB PHOSPHATE4PDGFRA
INFIGRATINIB4PDGFRA
REGORAFENIB4PDGFRA
CERITINIB4PDGFRA
VANDETANIB4PDGFRA
NILOTINIB4PDGFRA
BOSUTINIB4PDGFRA
NINTEDANIB ESYLATE4PDGFRA
PEXIDARTINIB4PDGFRA
AVAPRITINIB4PDGFRA
RIPRETINIB4PDGFRA
PAZOPANIB4PDGFRA
NINTEDANIB4PDGFRA
SUNITINIB4PDGFRA
DASATINIB4PDGFRA
ERLOTINIB4PDGFRA
QUIZARTINIB4PDGFRA
MIDOSTAURIN4PDGFRA
IMATINIB4PDGFRA
BEMPEDOIC ACID4ACACB
VATALANIB3PDGFRA
MASITINIB3PDGFRA
CRENOLANIB3PDGFRA

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)2PDGFRA, ACACB
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug8UBB, ARID5B, MORN5, MIB1, DENND4B, SATB2, GRHL3, ARHGAP29

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
UBB1
ARID5B0
MORN50
MIB10
DENND4B0
SATB26
GRHL30
ARHGAP290

Clinical trials & evidence

Clinical trials

Clinical trials: 0.