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Atlas / Disease / Advanced sleep phase syndrome 2

Advanced sleep phase syndrome 2

disease
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Also known as advanced sleep phase syndrome caused by mutation in CSNK1Dadvanced sleep phase syndrome type 2advanced sleep phase syndrome, familial, 2advanced sleep phase syndrome, familial, type 2advanced sleep-phase syndrome, familial, 2CSNK1D advanced sleep phase syndromeFASPS2

Summary

Advanced sleep phase syndrome 2 (MONDO:0014088) is a disease with 1 cohort gene.

At a glance

  • Cohort genes: 1
  • ClinVar variants: 2

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameadvanced sleep phase syndrome 2
Mondo IDMONDO:0014088
OMIM615224
DOIDDOID:0110012
UMLSC3808874
MedGen815204
GARD0015922
Is cancer (heuristic)no

Also known as: advanced sleep phase syndrome caused by mutation in CSNK1D · advanced sleep phase syndrome type 2 · advanced sleep phase syndrome, familial, 2 · advanced sleep phase syndrome, familial, type 2 · advanced sleep-phase syndrome, familial, 2 · CSNK1D advanced sleep phase syndrome · FASPS2

Data availability: 2 ClinVar variants.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › advanced sleep phase syndrome › advanced sleep phase syndrome 2

Related subtypes (3): advanced sleep phase syndrome 1, advanced sleep phase syndrome 3, advance sleep phase syndrome, familial, 4

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

2 retrieved; paginated sample, class counts are floors:

2 pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
50319NM_001893.6(CSNK1D):c.137A>G (p.His46Arg)CSNK1DPathogenicno assertion criteria provided
8741NM_001893.6(CSNK1D):c.130A>G (p.Thr44Ala)CSNK1DPathogenicno assertion criteria provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CSNK1DOrphanet:164736Familial advanced sleep-phase syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CSNK1DHGNC:2452ENSG00000141551P48730Casein kinase I isoform deltaclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CSNK1DCasein kinase I isoform deltaEssential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
Kinase127.7×0.036

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CSNK1DKinaseyes2.7.11.1Prot_kinase_dom, Ser/Thr_kinase_AS, Kinase-like_dom_sf

Expression context

Cohort genes with no expression data: 0.

1 cohort gene 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)1
unknown0

Top tissues across cohort

TissueCohort genes
left testis1
right testis1
small intestine Peyer’s patch1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CSNK1D299ubiquitousmarkerleft testis, right testis, small intestine Peyer’s patch

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CSNK1D2,741

Structural data

PDB: 1 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CSNK1DP4873046

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 31. Enrichment computed across 1 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Phosphorylation and nuclear translocation of the CRY:PER:kinase complex1815.7×0.016CSNK1D
The CRY:PER:kinase complex represses transactivation by the BMAL:CLOCK (ARNTL:CLOCK) complex1713.8×0.016CSNK1D
R-HSA-4002531346.1×0.016CSNK1D
Centrosome maturation1253.8×0.016CSNK1D
COPII-mediated vesicle transport1163.1×0.016CSNK1D
rRNA processing in the nucleus and cytosol1160.8×0.016CSNK1D
Loss of Nlp from mitotic centrosomes1158.6×0.016CSNK1D
Loss of proteins required for interphase microtubule organization from the centrosome1158.6×0.016CSNK1D
AURKA Activation by TPX21152.3×0.016CSNK1D
rRNA processing1146.4×0.016CSNK1D
Recruitment of mitotic centrosome proteins and complexes1135.9×0.016CSNK1D
ER to Golgi Anterograde Transport1132.8×0.016CSNK1D
Regulation of PLK1 Activity at G2/M Transition1126.9×0.016CSNK1D
Mitotic G2-G2/M phases1126.9×0.016CSNK1D
G2/M Transition1126.9×0.016CSNK1D
Recruitment of NuMA to mitotic centrosomes1116.5×0.016CSNK1D
Anchoring of the basal body to the plasma membrane1113.1×0.016CSNK1D
Cilium Assembly1108.8×0.016CSNK1D
Transport to the Golgi and subsequent modification1102.9×0.016CSNK1D
Mitotic Prometaphase169.2×0.021CSNK1D
Organelle biogenesis and maintenance166.0×0.021CSNK1D
M Phase166.0×0.021CSNK1D
Major pathway of rRNA processing in the nucleolus and cytosol161.7×0.021CSNK1D
Asparagine N-linked glycosylation160.1×0.021CSNK1D
Cell Cycle, Mitotic148.2×0.026CSNK1D
Metabolism of RNA141.7×0.029CSNK1D
Membrane Trafficking137.1×0.031CSNK1D
Cell Cycle136.0×0.031CSNK1D
Vesicle-mediated transport134.8×0.031CSNK1D
Post-translational protein modification119.2×0.054CSNK1D

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of non-canonical Wnt signaling pathway12106.5×0.005CSNK1D
midbrain dopaminergic neuron differentiation11203.7×0.005CSNK1D
protein localization to Golgi apparatus1802.5×0.005CSNK1D
COPII vesicle coat assembly1702.2×0.005CSNK1D
protein localization to centrosome1674.1×0.005CSNK1D
microtubule nucleation1624.1×0.005CSNK1D
spindle assembly1443.5×0.006CSNK1D
protein localization to cilium1401.2×0.006CSNK1D
non-motile cilium assembly1290.6×0.007CSNK1D
regulation of circadian rhythm1259.3×0.007CSNK1D
circadian regulation of gene expression1234.1×0.007CSNK1D
positive regulation of proteasomal ubiquitin-dependent protein catabolic process1210.7×0.007CSNK1D
positive regulation of canonical Wnt signaling pathway1154.6×0.009CSNK1D
Golgi organization1133.8×0.010CSNK1D
Wnt signaling pathway199.7×0.012CSNK1D
endocytosis195.2×0.012CSNK1D
protein phosphorylation168.0×0.016CSNK1D
signal transduction116.1×0.062CSNK1D

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 0

Druggability breadth: 1 of 1 evidence-associated genes (100%) 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
CSNK1DBOSUTINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
CSNK1D354

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BOSUTINIB4CSNK1D
NINTEDANIB4CSNK1D
SUNITINIB4CSNK1D
ERLOTINIB4CSNK1D
GEFITINIB4CSNK1D
LINIFANIB3CSNK1D
CANERTINIB3CSNK1D
DOVITINIB3CSNK1D
SILMITASERTIB2CSNK1D
SELICICLIB2CSNK1D
CC-4012CSNK1D
SU-0148132CSNK1D
ZOTIRACICLIB2CSNK1D
CENISERTIB2CSNK1D
ILORASERTIB2CSNK1D
DEFOSBARASERTIB2CSNK1D
TG100-1152CSNK1D
GALUNISERTIB2CSNK1D
TAK-7152CSNK1D
MW-1502CSNK1D
BI-25362CSNK1D
PICTILISIB2CSNK1D
MILCICLIB2CSNK1D
PELITINIB2CSNK1D
GSK-10709161CSNK1D
R-14871CSNK1D
KW-24491CSNK1D
HARMINE1CSNK1D
BMS-3870321CSNK1D
GSK-10596151CSNK1D

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
CSNK1D627Binding:622, Functional:4, ADMET:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
CSNK1D2.7.11.1, 2.7.11.26non-specific serine/threonine protein kinase, tau-protein kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
CSNK1D627

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; 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)
BOSUTINIB4CSNK1D
NINTEDANIB4CSNK1D
SUNITINIB4CSNK1D
ERLOTINIB4CSNK1D
GEFITINIB4CSNK1D
LINIFANIB3CSNK1D
CANERTINIB3CSNK1D
DOVITINIB3CSNK1D
SILMITASERTIB2CSNK1D
SELICICLIB2CSNK1D
CC-4012CSNK1D
SU-0148132CSNK1D
ZOTIRACICLIB2CSNK1D
CENISERTIB2CSNK1D
ILORASERTIB2CSNK1D
DEFOSBARASERTIB2CSNK1D
TG100-1152CSNK1D
GALUNISERTIB2CSNK1D
TAK-7152CSNK1D
MW-1502CSNK1D
BI-25362CSNK1D
PICTILISIB2CSNK1D
MILCICLIB2CSNK1D
PELITINIB2CSNK1D
GSK-10709161CSNK1D
R-14871CSNK1D
KW-24491CSNK1D
HARMINE1CSNK1D
BMS-3870321CSNK1D
GSK-10596151CSNK1D

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1CSNK1D
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 69

This page pulls from 69 datasets indexed by BioBTree:

alphafoldantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetcivic_evidenceclingen_dosageclinical_trialsclinvarctd_gene_interactiondepmapdiamond_similaritydoidefoensemblentrezesm2_similarityfantom5_genefantom5_promotergardgenccgenerifgogtopdbgtopdb_interactiongwasgwas_studyhgncintactinterpromedgenmeshmimmondomondochildmondoparentorphanetpatentpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assayreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorstring_interactiontranscriptufeatureumlsuniprot