Noonan syndrome 8

disease
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Also known as Noonan syndrome caused by mutation in RIT1Noonan syndrome type 8NS8RIT1 Noonan syndrome

Summary

Noonan syndrome 8 (MONDO:0014143) is a disease caused by RIT1 (GenCC Definitive), with 6 cohort genes.

At a glance

  • Causal gene: RIT1 (GenCC Definitive)
  • Cohort genes: 6
  • ClinVar variants: 307

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameNoonan syndrome 8
Mondo IDMONDO:0014143
OMIM615355
DOIDDOID:0060586
NCITC176936
UMLSC3809233
MedGen815563
GARD0015949
Is cancer (heuristic)no

Also known as: Noonan syndrome 8 · Noonan syndrome caused by mutation in RIT1 · Noonan syndrome type 8 · NS8 · RIT1 Noonan syndrome

Data availability: 307 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic diseaseNoonan syndromeNoonan syndrome 8

Related subtypes (13): Noonan syndrome 1, Noonan syndrome 2, Noonan syndrome 3, Noonan syndrome 4, Noonan syndrome 5, Noonan syndrome 6, Noonan syndrome 7, Noonan syndrome 9, Noonan syndrome 10, Noonan syndrome 14, Noonan syndrome 11, noonan syndrome 12, Noonan syndrome 13

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

307 retrieved; paginated sample, class counts are floors:

136 uncertain significance, 108 likely benign, 20 conflicting classifications of pathogenicity, 17 pathogenic, 15 pathogenic/likely pathogenic, 4 benign, 4 likely pathogenic, 3 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
2425657NC_000001.10:g.(?155581953)(155880552_?)delDAP3Pathogeniccriteria provided, single submitter
376489NM_006218.4(PIK3CA):c.1034A>C (p.Asn345Thr)PIK3CAPathogeniccriteria provided, single submitter
120250NM_006912.6(RIT1):c.270G>A (p.Met90Ile)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1695891NM_006912.6(RIT1):c.67A>G (p.Lys23Glu)RIT1Pathogeniccriteria provided, single submitter
181522NM_006912.6(RIT1):c.246T>G (p.Phe82Leu)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
183401NM_006912.6(RIT1):c.104G>C (p.Ser35Thr)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
183403NM_006912.6(RIT1):c.229G>A (p.Ala77Thr)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
183404NM_006912.6(RIT1):c.241G>C (p.Glu81Gln)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
183405NM_006912.6(RIT1):c.242A>G (p.Glu81Gly)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
183406NM_006912.6(RIT1):c.244T>A (p.Phe82Ile)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
183407NM_006912.6(RIT1):c.244T>C (p.Phe82Leu)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
183408NM_006912.6(RIT1):c.244T>G (p.Phe82Val)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
183409NM_006912.6(RIT1):c.247A>C (p.Thr83Pro)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
183410NM_006912.6(RIT1):c.251C>T (p.Ala84Val)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
183411NM_006912.6(RIT1):c.265T>C (p.Tyr89His)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
190305NM_006912.6(RIT1):c.270G>C (p.Met90Ile)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
224122NM_006912.6(RIT1):c.67A>C (p.Lys23Gln)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
228289NM_006912.6(RIT1):c.229G>C (p.Ala77Pro)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2431215NM_006912.6(RIT1):c.111G>C (p.Met37Ile)RIT1Pathogeniccriteria provided, single submitter
265328NM_006912.6(RIT1):c.270G>T (p.Met90Ile)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
280151NM_006912.6(RIT1):c.259G>C (p.Asp87His)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
280609NM_006912.6(RIT1):c.365G>T (p.Arg122Leu)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3382471NM_006912.6(RIT1):c.269T>C (p.Met90Thr)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
370035NM_006912.6(RIT1):c.246T>A (p.Phe82Leu)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
372863NM_006912.6(RIT1):c.245T>G (p.Phe82Cys)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
561621NM_006912.6(RIT1):c.229G>T (p.Ala77Ser)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
561681NM_006912.6(RIT1):c.268A>G (p.Met90Val)RIT1Pathogenicreviewed by expert panel
581105NM_006912.6(RIT1):c.69A>C (p.Lys23Asn)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts
60506NM_006912.6(RIT1):c.170C>G (p.Ala57Gly)RIT1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
60509NM_006912.6(RIT1):c.284G>C (p.Gly95Ala)RIT1Pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 16 · 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
RIT1DefinitiveAutosomal dominantNoonan syndrome6

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
RIT1Orphanet:648Noonan syndrome
PIK3CAOrphanet:140944CLOVES syndrome
PIK3CAOrphanet:144Lynch syndrome
PIK3CAOrphanet:168984CLAPO syndrome
PIK3CAOrphanet:201Cowden syndrome
PIK3CAOrphanet:210159Adult hepatocellular carcinoma
PIK3CAOrphanet:221061Familial cerebral cavernous malformation
PIK3CAOrphanet:2495Meningioma
PIK3CAOrphanet:276280Hemihyperplasia-multiple lipomatosis syndrome
PIK3CAOrphanet:295239Macrodactyly of fingers, unilateral
PIK3CAOrphanet:295243Macrodactyly of toes, unilateral
PIK3CAOrphanet:314662Segmental progressive overgrowth syndrome with fibroadipose hyperplasia
PIK3CAOrphanet:60040Megalencephaly-capillary malformation-polymicrogyria syndrome
PIK3CAOrphanet:714737Diffuse capillary malformation with overgrowth
PIK3CAOrphanet:90308Capillary-lymphatic-venous malformation with segmental distribution
PIK3CAOrphanet:99802Hemimegalencephaly

Cohort genes → proteins

6 cohort genes, 5 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
RIT1HGNC:10023ENSG00000143622Q92963GTP-binding protein Rit1gencc,clinvar
DAP3HGNC:2673ENSG00000132676P51398Small ribosomal subunit protein mS29clinvar
DLGAP3HGNC:30368ENSG00000116544O95886Disks large-associated protein 3clinvar
HSH2D-AS1HGNC:58332ENSG00000269243HSH2D and RAB8A antisense RNA 1clinvar
ARHGEF2HGNC:682ENSG00000116584Q92974Rho guanine nucleotide exchange factor 2clinvar
PIK3CAHGNC:8975ENSG00000121879P42336Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
RIT1GTP-binding protein Rit1Plays a crucial role in coupling NGF stimulation to the activation of both EPHB2 and MAPK14 signaling pathways and in NGF-dependent neuronal differentiation.
DAP3Small ribosomal subunit protein mS29As a component of the mitochondrial small ribosomal subunit, it plays a role in the translation of mitochondrial mRNAs.
DLGAP3Disks large-associated protein 3May play a role in the molecular organization of synapses and neuronal cell signaling.
ARHGEF2Rho guanine nucleotide exchange factor 2Activates Rho-GTPases by promoting the exchange of GDP for GTP.
PIK3CAPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformPhosphoinositide-3-kinase (PI3K) phosphorylates phosphatidylinositol (PI) and its phosphorylated derivatives at position 3 of the inositol ring to produce 3-phosphoinositides.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 4 · Druggable fraction: 0.17

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
Kinase14.6×0.451
Scaffold/PPI12.9×0.451
Other/Unknown41.2×0.458

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
RIT1Other/UnknownnoSmall_GTPase, Small_GTP-bd, Small_GTPase_Ras-type
DAP3Other/UnknownnoRibosomal_mS29_met, Ribosomal_mS29, P-loop_NTPase
DLGAP3Other/UnknownnoSAPAP
HSH2D-AS1Other/Unknownno
ARHGEF2Scaffold/PPInoDH_dom, PH_domain, PKC_DAG/PE
PIK3CAKinaseyes2.7.1.137PI3K_Ras-bd_dom, PI3/4_kinase_cat_dom, PI3K_accessory_dom

Expression context

Cohort genes with no expression data: 0.

4 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)6
unknown0

Top tissues across cohort

TissueCohort genes
adrenal tissue2
leukocyte1
monocyte1
mononuclear cell1
body of pancreas1
colonic epithelium1
anterior cingulate cortex1
nucleus accumbens1
right frontal lobe1
bone marrow cell1
granulocyte1
mucosa of transverse colon1
corpus callosum1
ganglionic eminence1
inferior vagus X ganglion1
calcaneal tendon1
tendon1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
RIT1268ubiquitousmarkermonocyte, mononuclear cell, leukocyte
DAP3294ubiquitousmarkerbody of pancreas, adrenal tissue, colonic epithelium
DLGAP3150broadyesright frontal lobe, anterior cingulate cortex, nucleus accumbens
HSH2D-AS1133yesmucosa of transverse colon, granulocyte, bone marrow cell
ARHGEF2297ubiquitousmarkerinferior vagus X ganglion, ganglionic eminence, corpus callosum
PIK3CA284ubiquitousmarkercalcaneal tendon, adrenal tissue, tendon

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PIK3CA5,157
DAP33,504
RIT13,298
ARHGEF22,202
DLGAP31,613
HSH2D-AS10

Structural data

PDB: 4 · AlphaFold-only: 1 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PIK3CAP42336135
DAP3P5139877
ARHGEF2Q9297460
RIT1Q929633

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
DLGAP3O9588650.83

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 82. Enrichment computed across 6 evidence-associated genes (5 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 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Signalling to p38 via RIT and RIN1456.8×0.026RIT1
MET activates PI3K/AKT signaling1380.7×0.026PIK3CA
Activated NTRK3 signals through PI3K1380.7×0.026PIK3CA
Activated NTRK2 signals through PI3K1326.3×0.026PIK3CA
Signaling by LTK in cancer1326.3×0.026PIK3CA
PI3K/AKT activation1253.8×0.026PIK3CA
IRS-mediated signalling1207.6×0.026PIK3CA
PI3K events in ERBB4 signaling1207.6×0.026PIK3CA
Co-stimulation by ICOS1207.6×0.026PIK3CA
Signaling by FGFR4 in disease1190.3×0.026PIK3CA
Erythropoietin activates Phosphoinositide-3-kinase (PI3K)1190.3×0.026PIK3CA
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants1175.7×0.026PIK3CA
Signaling by PDGFRA extracellular domain mutants1175.7×0.026PIK3CA
Signaling by LTK1175.7×0.026PIK3CA
Signaling by FLT3 ITD and TKD mutants1152.3×0.026PIK3CA
Constitutive Signaling by EGFRvIII1142.8×0.026PIK3CA
PI3K events in ERBB2 signaling1134.3×0.026PIK3CA
Signaling by ERBB2 ECD mutants1134.3×0.026PIK3CA
GAB1 signalosome1126.9×0.026PIK3CA
Signaling by cytosolic FGFR1 fusion mutants1126.9×0.026PIK3CA
PI-3K cascade:FGFR31126.9×0.026PIK3CA
Tie2 Signaling1120.2×0.026PIK3CA
Role of LAT2/NTAL/LAB on calcium mobilization1120.2×0.026PIK3CA
Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants1114.2×0.026PIK3CA
Signaling by ALK1114.2×0.026PIK3CA
PI-3K cascade:FGFR41114.2×0.026PIK3CA
Signaling by FLT3 fusion proteins1114.2×0.026PIK3CA
PI-3K cascade:FGFR11103.8×0.026PIK3CA
Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants1103.8×0.026PIK3CA
PI-3K cascade:FGFR2199.3×0.026PIK3CA

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
response to muscle inactivity13370.4×0.012PIK3CA
response to butyrate13370.4×0.012PIK3CA
response to L-leucine11123.5×0.014PIK3CA
asymmetric neuroblast division11123.5×0.014ARHGEF2
cellular response to hydrostatic pressure11123.5×0.014PIK3CA
negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress1842.6×0.015ARHGEF2
negative regulation of actin filament depolymerization1561.7×0.015PIK3CA
regulation of cellular respiration1561.7×0.015PIK3CA
regulation of actin filament organization1481.5×0.015PIK3CA
autosome genomic imprinting1481.5×0.015PIK3CA
negative regulation of fibroblast apoptotic process1481.5×0.015PIK3CA
modification of postsynaptic structure1374.5×0.015DLGAP3
cellular response to muramyl dipeptide1337.0×0.015ARHGEF2
cardiac muscle cell contraction1337.0×0.015PIK3CA
positive regulation of protein localization to membrane1337.0×0.015PIK3CA
signaling1306.4×0.015DLGAP3
TORC2 signaling1306.4×0.015PIK3CA
phosphatidylinositol-3-phosphate biosynthetic process1259.3×0.015PIK3CA
anoikis1259.3×0.015PIK3CA
relaxation of cardiac muscle1259.3×0.015PIK3CA
cellular hyperosmotic response1240.7×0.015ARHGEF2
response to dexamethasone1240.7×0.015PIK3CA
vasculature development1224.7×0.015PIK3CA
negative regulation of macroautophagy1224.7×0.015PIK3CA
vascular endothelial growth factor signaling pathway1210.7×0.015PIK3CA
negative regulation of necroptotic process1198.3×0.015ARHGEF2
positive regulation of neuron migration1198.3×0.015ARHGEF2
apoptotic mitochondrial changes1177.4×0.015DAP3
negative regulation of anoikis1177.4×0.015PIK3CA
positive regulation of peptidyl-tyrosine phosphorylation1160.5×0.016ARHGEF2

Therapeutics

Drug target analysis

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

Druggability breadth: 3 of 6 evidence-associated genes (50%) 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
PIK3CAIDELALISIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
PIK3CA674
ARHGEF212
RIT100
DAP300
DLGAP300
HSH2D-AS100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IDELALISIB4PIK3CA
ALPELISIB4PIK3CA
DUVELISIB4PIK3CA
COPANLISIB4PIK3CA
FEDRATINIB4PIK3CA
ROMIDEPSIN4PIK3CA
COPANLISIB HYDROCHLORIDE4PIK3CA
LENIOLISIB4PIK3CA
BELINOSTAT4PIK3CA
INAVOLISIB4PIK3CA
SUNITINIB4PIK3CA
DASATINIB4PIK3CA
CRIZOTINIB4PIK3CA
MIDOSTAURIN4PIK3CA
DACTOLISIB3PIK3CA
BUPARLISIB3PIK3CA
RESVERATROL3PIK3CA
IPATASERTIB3PIK3CA
TASELISIB3PIK3CA
EPIGALOCATECHIN GALLATE3PIK3CA
GEDATOLISIB3PIK3CA
LESTAURTINIB3PIK3CA
MOLIBRESIB2ARHGEF2
OMIPALISIB2PIK3CA
VISTUSERTIB2PIK3CA
FIMEPINOSTAT2PIK3CA
EGANELISIB2PIK3CA
BERZOSERTIB2PIK3CA
BIMIRALISIB2PIK3CA
PICTILISIB2PIK3CA

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
PIK3CA2,034Binding:2009, ADMET:19, Toxicity:4, Functional:2
ARHGEF28Binding:8
DAP32Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
PIK3CA2.7.1.137, 2.7.1.153, 2.7.11.1phosphatidylinositol 3-kinase, phosphatidylinositol-4,5-bisphosphate 3-kinase, non-specific serine/threonine protein kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
PIK3CA2,034

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; 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)
IDELALISIB4PIK3CA
ALPELISIB4PIK3CA
DUVELISIB4PIK3CA
COPANLISIB4PIK3CA
FEDRATINIB4PIK3CA
ROMIDEPSIN4PIK3CA
COPANLISIB HYDROCHLORIDE4PIK3CA
LENIOLISIB4PIK3CA
BELINOSTAT4PIK3CA
INAVOLISIB4PIK3CA
SUNITINIB4PIK3CA
DASATINIB4PIK3CA
CRIZOTINIB4PIK3CA
MIDOSTAURIN4PIK3CA
DACTOLISIB3PIK3CA
BUPARLISIB3PIK3CA
RESVERATROL3PIK3CA
IPATASERTIB3PIK3CA
TASELISIB3PIK3CA
EPIGALOCATECHIN GALLATE3PIK3CA
GEDATOLISIB3PIK3CA
LESTAURTINIB3PIK3CA
MOLIBRESIB2ARHGEF2
OMIPALISIB2PIK3CA
VISTUSERTIB2PIK3CA
FIMEPINOSTAT2PIK3CA
EGANELISIB2PIK3CA
BERZOSERTIB2PIK3CA
BIMIRALISIB2PIK3CA
PICTILISIB2PIK3CA

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PIK3CA
BPhased (≥1) drug, not yet approved1ARHGEF2
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4RIT1, DAP3, DLGAP3, HSH2D-AS1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
RIT10
DAP32
DLGAP30
HSH2D-AS10

Clinical trials & evidence

Clinical trials

Clinical trials: 0.