autosomal recessive Kenny-Caffey syndrome

disease
On this page

Also known as KCS1Kenny-Caffey syndrome type 1Kenny-Caffey syndrome, autosomal recessiveKenny-Caffey syndrome, type 1

Summary

autosomal recessive Kenny-Caffey syndrome (MONDO:0009486) is a disease with 2 cohort genes.

At a glance

  • Cohort genes: 2
  • ClinVar variants: 23
  • Phenotypes (HPO): 22

Clinical features

Signs & symptoms

Clinical features (HPO)

22 HPO clinical features (Orphanet curated; top 22 by frequency):

HPO IDTermFrequency
HP:0002199Hypocalcemic seizuresVery frequent (80-99%)
HP:0002901HypocalcemiaVery frequent (80-99%)
HP:0008198Congenital hypoparathyroidismVery frequent (80-99%)
HP:0000252MicrocephalyFrequent (30-79%)
HP:0000270Delayed cranial suture closureFrequent (30-79%)
HP:0000293Full cheeksFrequent (30-79%)
HP:0000316HypertelorismFrequent (30-79%)
HP:0000670Carious teethFrequent (30-79%)
HP:0000883Thin ribsFrequent (30-79%)
HP:0001510Growth delayFrequent (30-79%)
HP:0001511Intrauterine growth retardationFrequent (30-79%)
HP:0001773Short footFrequent (30-79%)
HP:0002750Delayed skeletal maturationFrequent (30-79%)
HP:0003472Hypocalcemic tetanyFrequent (30-79%)
HP:0004331Decreased skull ossificationFrequent (30-79%)
HP:0005450Calvarial osteosclerosisFrequent (30-79%)
HP:0005791Cortical thickening of long bone diaphysesFrequent (30-79%)
HP:0006470Thin long bone diaphysesFrequent (30-79%)
HP:0006645Thin claviclesFrequent (30-79%)
HP:0008897Postnatal growth retardationFrequent (30-79%)
HP:0100254Stenosis of the medullary cavity of the long bonesFrequent (30-79%)
HP:0200055Small handFrequent (30-79%)

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal recessive Kenny-Caffey syndrome
Mondo IDMONDO:0009486
MeSHC537021
OMIM244460
Orphanet93324
DOIDDOID:0080722
NCITC130992
UMLSC1855648
MedGen340923
GARD0008367
Is cancer (heuristic)no

Also known as: KCS1 · Kenny-Caffey syndrome type 1 · Kenny-Caffey syndrome, autosomal recessive · Kenny-Caffey syndrome, type 1

Data availability: 23 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive diseaseautosomal recessive Kenny-Caffey syndrome

Related subtypes (218): immunodeficiency-centromeric instability-facial anomalies syndrome, hypercalcemia, infantile, Ochoa syndrome, autosomal recessive Ehlers-Danlos syndrome, vascular type, hydrolethalus syndrome, 3-M syndrome, isolated hyperchlorhidrosis, dacryocystitis-osteopoikilosis syndrome, Hutchinson-Gilford progeria syndrome, achalasia microcephaly syndrome, acrorenal syndrome, autosomal recessive, beta-ketothiolase deficiency, autosomal recessive Alport syndrome, Alstrom syndrome, microphthalmia with limb anomalies, camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Behr syndrome, bifid nose, autosomal recessive, Bloom syndrome, Bowen-Conradi syndrome, camptodactyly with fibrous tissue hyperplasia and skeletal dysplasia, heart defects-limb shortening syndrome, autosomal recessive palmoplantar keratoderma and congenital alopecia, COFS syndrome, craniometaphyseal dysplasia, autosomal recessive, Fraser syndrome, cystic fibrosis, polycystic lipomembranous osteodysplasia with sclerosing leukoencephaly, persistent hyperplastic primary vitreous, autosomal recessive, Donnai-Barrow syndrome, Schöpf-Schulz-Passarge syndrome, cleft lip/palate-ectodermal dysplasia syndrome, Ellis-van Creveld syndrome, Wolcott-Rallison syndrome, autosomal recessive faciodigitogenital syndrome, acromesomelic dysplasia 2B, brittle cornea syndrome, triple-A syndrome, autosomal recessive humeroradial synostosis, multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome, hydrocephalus, nonsyndromic, autosomal recessive 1, autosomal recessive hydrocephalus due to congenital stenosis of aqueduct of Sylvius, hypertelorism, microtia, facial clefting syndrome, hypoparathyroidism-retardation-dysmorphism syndrome, Vici syndrome, Johanson-Blizzard syndrome, Papillon-Lefevre disease, Haim-Munk syndrome, Laurence-Moon syndrome, Donohue syndrome, lipase deficiency, combined, autosomal recessive familial Mediterranean fever, thiamine-responsive megaloblastic anemia syndrome, cartilage-hair hypoplasia, Nijmegen breakage syndrome, pseudo-TORCH syndrome, Galloway-Mowat syndrome, mulibrey nanism, myotonia congenita, autosomal recessive, Schwartz-Jampel syndrome, proteosome-associated autoinflammatory syndrome, Netherton syndrome, Niemann-Pick disease type A, oculodentodigital dysplasia, autosomal recessive, odonto-onycho-dermal dysplasia, autosomal recessive omodysplasia, osteoporosis-pseudoglioma syndrome, Shwachman-Diamond syndrome, phenylketonuria, Bjornstad syndrome, Laron syndrome, autosomal recessive polycystic kidney disease, autosomal recessive inherited pseudoxanthoma elasticum, autosomal recessive multiple pterygium syndrome, rapadilino syndrome, short-rib thoracic dysplasia 9 with or without polydactyly, autosomal recessive Robinow syndrome, Sjogren-Larsson syndrome, scapuloperoneal spinal muscular atrophy, autosomal recessive, spondyloepiphyseal dysplasia tarda, autosomal recessive, inherited threoninemia, Pendred syndrome, autosomal recessive spondylocostal dysostosis, Werner syndrome, ABCD syndrome, Naxos disease, autosomal recessive amelia, human HOXA1 syndromes, sickle cell disease, autosomal recessive proximal renal tubular acidosis, hyper-IgM syndrome type 2, temtamy preaxial brachydactyly syndrome, TH-deficient dopa-responsive dystonia, craniosynostosis syndrome, autosomal recessive, Niemann-Pick disease type B, skin fragility-woolly hair-palmoplantar keratoderma syndrome, CoQ-responsive OXPHOS deficiency, familial adenomatous polyposis 2, Pierson syndrome, palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome, cardiomyopathy-hypotonia-lactic acidosis syndrome, PHARC syndrome, Kahrizi syndrome, cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies, congenital prothrombin deficiency, immunodeficiency 31B, dyskeratosis congenita, autosomal recessive 2, dyskeratosis congenita, autosomal recessive 3, Nestor-Guillermo progeria syndrome, leukoencephalopathy with calcifications and cysts, mitochondrial pyruvate carrier deficiency, branched-chain keto acid dehydrogenase kinase deficiency, dyskeratosis congenita, autosomal recessive 5, hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome, alacrima, achalasia, and intellectual disability syndrome, hyperlipoproteinemia, type 1D, microcephaly and chorioretinopathy 2, congenital stationary night blindness 1G, combined oxidative phosphorylation deficiency 29, hypermanganesemia with dystonia 2, growth retardation, intellectual developmental disorder, hypotonia, and hepatopathy, gnb5-related intellectual disability-cardiac arrhythmia syndrome, autosomal recessive spastic paraplegia type 78, autosomal recessive limb-girdle muscular dystrophy, Bardet-Biedl syndrome, autosomal recessive cerebellar ataxia, neuronopathy, distal hereditary motor, autosomal recessive, UV-sensitive syndrome, Ehlers-Danlos syndrome, kyphoscoliotic type 1, Cockayne syndrome, hyperphenylalaninemia due to tetrahydrobiopterin deficiency, leukoencephalopathy-palmoplantar keratoderma syndrome, autosomal recessive hypohidrotic ectodermal dysplasia, Warburg micro syndrome, autosomal recessive primary microcephaly, autosomal recessive progressive external ophthalmoplegia, Meier-Gorlin syndrome, autosomal recessive sideroblastic anemia, autosomal recessive intermediate Charcot-Marie-Tooth disease, Perrault syndrome, autosomal recessive hypophosphatemic rickets, de Barsy syndrome, leukocyte adhesion deficiency, Senior-Loken syndrome, autosomal recessive spastic ataxia, childhood-onset autosomal recessive myopathy with external ophthalmoplegia, autosomal recessive cerebral atrophy, GM3 synthase deficiency, autosomal recessive distal renal tubular acidosis, pigmentation defects-palmoplantar keratoderma-skin carcinoma syndrome, autosomal recessive brachyolmia, Aicardi-Goutieres syndrome, homocystinuria without methylmalonic aciduria, Niemann-Pick disease type C, nephronophthisis, autosomal recessive osteopetrosis, peroxisome biogenesis disorder, congenital non-bullous ichthyosiform erythroderma, Seckel syndrome, Usher syndrome, autosomal recessive cutis laxa type 1, autosomal recessive cutis laxa type 2, hearing loss, autosomal recessive, microcephaly, growth restriction, and increased sister chromatid exchange 2, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 1, congenital vertebral-cardiac-renal anomalies syndrome, hair defect with photosensitivity and intellectual disability syndrome, autosomal recessive severe congenital neutropenia, severe combined immunodeficiency due to CARMIL2 deficiency, extraoral halitosis due to methanethiol oxidase deficiency, neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities, mitochondrial complex 2 deficiency, nuclear type 3, mitochondrial complex 2 deficiency, nuclear type 4, mismatch repair cancer syndrome, spondyloepimetaphyseal dysplasia with joint laxity, type 3, Kilquist syndrome, Duane anomaly-myopathy-scoliosis syndrome, autosomal recessive axonal charcot-marie-tooth disease due to copper metabolism defect, immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections-lymphopenia syndrome, optic atrophy-ataxia-peripheral neuropathy-global developmental delay syndrome, congenital myopathy with reduced type 2 muscle fibers, NAD(P)HX dehydratase deficiency, autosomal recessive ocular albinism, ichthyosis linearis circumflexa, eosinophil peroxidase deficiency, hyperphenylalaninemia due to DNAJC12 deficiency, autosomal recessive epidermolytic ichthyosis, Ehlers-Danlos syndrome, classic-like, 2, joint laxity, short stature, and myopia, HELIX syndrome, auditory neuropathy-optic atrophy syndrome, glycosylphosphatidylinositol biosynthesis defect 15, neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures, SCN4A-related myopathy, autosomal recessive, Uner Tan Syndrome, nephropathic cystinosis, Imerslund-Grasbeck syndrome type 1, Imerslund-Grasbeck syndrome type 2, permanent neonatal diabetes mellitus 1, growth hormone insensitivity with immune dysregulation 1, autosomal recessive, Rajab interstitial lung disease with brain calcifications 1, Roberts-SC phocomelia syndrome, neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities, RPE65-related recessive retinopathy, GUCY2D-related recessive retinopathy, autosomal recessive titinopathy, intellectual disability, autosomal recessive, ALPL-related autosomal recessive hypophosphatasia, spastic paraplegia 18b, autosomal recessive, CEP164-related ciliopathy, RP1-related recessive retinopathy, pseudohypoaldosteronism, type IB2, autosomal recessive, pseudohypoaldosteronism, type IB3, autosomal recessive, spastic paraplegia 30B, autosomal recessive, cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1, brain small vessel disease 2B, autosomal recessive, IMPG1-related recessive retinopathy, PROM1-related recessive retinopathy

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

23 retrieved; paginated sample, class counts are floors:

7 uncertain significance, 7 likely pathogenic, 5 pathogenic/likely pathogenic, 4 conflicting classifications of pathogenicity

ClinVarVariant (HGVS)GeneClassificationReview
225483NM_003193.5(TBCE):c.143_144del (p.Lys48fs)TBCEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
2743364NM_003193.5(TBCE):c.433A>T (p.Lys145Ter)TBCEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
5290NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del)TBCEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
631595NM_003193.5(TBCE):c.100+1G>ATBCEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
804381NM_003193.5(TBCE):c.355_356del (p.Ile119fs)TBCEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1297492NM_003193.5(TBCE):c.101-1G>CTBCELikely pathogeniccriteria provided, single submitter
3581407NM_003193.5(TBCE):c.34C>T (p.Arg12Ter)TBCELikely pathogeniccriteria provided, single submitter
3581420NM_003193.5(TBCE):c.185+1G>CTBCELikely pathogeniccriteria provided, single submitter
3581427NM_003193.5(TBCE):c.561-2A>GTBCELikely pathogeniccriteria provided, single submitter
3581430NM_003193.5(TBCE):c.736del (p.Arg246fs)TBCELikely pathogeniccriteria provided, single submitter
3581434NM_003193.5(TBCE):c.1116+1G>TTBCELikely pathogeniccriteria provided, single submitter
870974NM_003193.5(TBCE):c.1038del (p.Glu347fs)TBCELikely pathogeniccriteria provided, multiple submitters, no conflicts
282266NM_003193.5(TBCE):c.1465C>A (p.Leu489Ile)B3GALNT2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
520625NM_003193.5(TBCE):c.1491_1491+4dupB3GALNT2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
193652NM_003193.5(TBCE):c.847A>T (p.Ile283Phe)TBCEConflicting classifications of pathogenicitycriteria provided, conflicting classifications
2189908NM_003193.5(TBCE):c.371+2_371+8dupTBCEConflicting classifications of pathogenicitycriteria provided, conflicting classifications
1033981NM_003193.5(TBCE):c.71G>A (p.Arg24His)TBCEUncertain significancecriteria provided, multiple submitters, no conflicts
1386786NM_003193.5(TBCE):c.581C>T (p.Pro194Leu)TBCEUncertain significancecriteria provided, multiple submitters, no conflicts
1449541NM_003193.5(TBCE):c.898+6T>CTBCEUncertain significancecriteria provided, multiple submitters, no conflicts
1709569NM_003193.5(TBCE):c.786T>G (p.Asn262Lys)TBCEUncertain significancecriteria provided, multiple submitters, no conflicts
3581423NM_003193.5(TBCE):c.389A>G (p.Gln130Arg)TBCEUncertain significancecriteria provided, single submitter
3892603NM_003193.5(TBCE):c.1112G>A (p.Cys371Tyr)TBCEUncertain significancecriteria provided, multiple submitters, no conflicts
3892605NM_003193.5(TBCE):c.661-1147A>GTBCEUncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 10 · Orphanet: 6 · 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
TBCEModerateAutosomal recessiveautosomal recessive Kenny-Caffey syndrome10

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TBCEOrphanet:2323Sanjad-Sakati syndrome
TBCEOrphanet:496756Early-onset progressive encephalopathy-spastic ataxia-distal spinal muscular atrophy syndrome
TBCEOrphanet:93324Autosomal recessive Kenny-Caffey syndrome
B3GALNT2Orphanet:588Muscle-eye-brain disease
B3GALNT2Orphanet:88616Autosomal recessive non-syndromic intellectual disability
B3GALNT2Orphanet:899Walker-Warburg syndrome

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TBCEHGNC:11582ENSG00000284770Q15813Tubulin-specific chaperone Egencc,clinvar
B3GALNT2HGNC:28596ENSG00000162885Q8NCR0UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TBCETubulin-specific chaperone ETubulin-folding protein; involved in the second step of the tubulin folding pathway and in the regulation of tubulin heterodimer dissociation.
B3GALNT2UDP-GalNAc:beta-1,3-N-acetylgalactosaminyltransferase 2Beta-1,3-N-acetylgalactosaminyltransferase that synthesizes a unique carbohydrate structure, GalNAc-beta-1-3GlcNAc, on N- and O-glycans.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.5

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
Enzyme (other)16.0×0.320
Other/Unknown10.9×0.805

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TBCEOther/UnknownnoUbiquitin-like_dom, CAP-Gly_domain, Ubiquitin-like_domsf
B3GALNT2Enzyme (other)yes2.4.1.313Glyco_trans_31

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)2
unknown0

Top tissues across cohort

TissueCohort genes
cortical plate1
hindlimb stylopod muscle1
ventricular zone1
adrenal tissue1
body of pancreas1
skeletal muscle tissue1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TBCE134ubiquitousyesventricular zone, hindlimb stylopod muscle, cortical plate
B3GALNT2141ubiquitousmarkerbody of pancreas, skeletal muscle tissue, adrenal tissue

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TBCE1,068
B3GALNT2748

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
TBCEQ158136

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
B3GALNT2Q8NCR086.81

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 6. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
DAG1 core M3 glycosylations1951.7×0.006B3GALNT2
Post-chaperonin tubulin folding pathway1237.9×0.012TBCE
Protein folding1129.8×0.012TBCE
Metabolism of proteins212.4×0.012TBCE, B3GALNT2
O-linked glycosylation172.3×0.017B3GALNT2
Post-translational protein modification19.6×0.101B3GALNT2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
muscle atrophy14213.0×0.003TBCE
peripheral nervous system neuron axonogenesis12106.5×0.003TBCE
post-chaperonin tubulin folding pathway11404.3×0.003TBCE
tubulin complex assembly1842.6×0.004TBCE
developmental growth1366.4×0.007TBCE
glycoprotein biosynthetic process1168.5×0.011B3GALNT2
adult locomotory behavior1150.5×0.011TBCE
mitotic spindle organization1135.9×0.011TBCE
protein O-linked glycosylation1112.3×0.012B3GALNT2
post-embryonic development1102.8×0.012TBCE
microtubule cytoskeleton organization160.6×0.018TBCE
protein folding151.7×0.019TBCE

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
TBCE00
B3GALNT200

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
B3GALNT22.4.1.313protein O-mannose beta-1,3-N-acetylgalactosaminyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug1B3GALNT2
EDifficult family or no structure, no drug1TBCE

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
TBCE0
B3GALNT20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.