Kilquist syndrome

disease
On this page

Also known as KILQSSLC12A2-related autosomal recessive neonatal-developmental delay-intellectual disability-feeding difficulty-sensorineural deafness syndrome

Summary

Kilquist syndrome (MONDO:0033664) is a disease caused by SLC12A2 (GenCC Strong), with 1 cohort gene.

At a glance

  • Causal gene: SLC12A2 (GenCC Strong)
  • Cohort genes: 1
  • ClinVar variants: 51

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameKilquist syndrome
Mondo IDMONDO:0033664
OMIM619080
Orphanet633021
UMLSC5436756
MedGen1742639
GARD0027953
Is cancer (heuristic)no

Also known as: KILQS · SLC12A2-related autosomal recessive neonatal-developmental delay-intellectual disability-feeding difficulty-sensorineural deafness syndrome

Data availability: 51 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 diseaseKilquist 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, autosomal recessive Kenny-Caffey 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, 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

51 retrieved; paginated sample, class counts are floors:

19 uncertain significance, 10 benign/likely benign, 8 likely benign, 6 conflicting classifications of pathogenicity, 5 pathogenic, 2 likely pathogenic, 1 benign

ClinVarVariant (HGVS)GeneClassificationReview
3064190NM_001046.3(SLC12A2):c.2617-2A>GSLC12A2Pathogeniccriteria provided, single submitter
617506Single alleleSLC12A2Pathogeniccriteria provided, single submitter
984662NM_001046.3(SLC12A2):c.1431del (p.Phe477fs)SLC12A2Pathogenicno assertion criteria provided
984663NM_001046.3(SLC12A2):c.2006-1G>ASLC12A2Pathogenicno assertion criteria provided
984673NC_000005.9:g.127441491_127471419delinsATGAAAAGCTTTACAGAAGTTGGAATTAAAAAAASLC12A2Pathogenicno assertion criteria provided
3064984NM_001046.3(SLC12A2):c.959C>A (p.Ser320Ter)SLC12A2Likely pathogeniccriteria provided, single submitter
3780607NM_001046.3(SLC12A2):c.3147G>A (p.Trp1049Ter)SLC12A2Likely pathogeniccriteria provided, single submitter
1385353NM_001046.3(SLC12A2):c.288GGC[10] (p.Ala105_Ala107dup)LOC129994526Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1335592NM_001046.3(SLC12A2):c.953-7C>TSLC12A2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1671022NM_001046.3(SLC12A2):c.562GGC[6] (p.Gly192dup)SLC12A2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1941803NM_001046.3(SLC12A2):c.2894C>A (p.Ser965Tyr)SLC12A2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2169828NM_001046.3(SLC12A2):c.476C>T (p.Ala159Val)SLC12A2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2287133NM_001046.3(SLC12A2):c.3134C>T (p.Thr1045Ile)SLC12A2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1365125NM_001046.3(SLC12A2):c.41G>T (p.Gly14Val)LOC129994526Uncertain significancecriteria provided, multiple submitters, no conflicts
1440806NM_001046.3(SLC12A2):c.288GGC[11] (p.Ala104_Ala107dup)LOC129994526Uncertain significancecriteria provided, multiple submitters, no conflicts
1510335NM_001046.3(SLC12A2):c.235A>C (p.Ser79Arg)LOC129994526Uncertain significancecriteria provided, multiple submitters, no conflicts
1373721NM_001046.3(SLC12A2):c.3622C>G (p.Leu1208Val)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1385672NM_001046.3(SLC12A2):c.788A>C (p.Glu263Ala)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1401954NM_001046.3(SLC12A2):c.2293C>G (p.Leu765Val)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1445687NM_001046.3(SLC12A2):c.2848G>A (p.Val950Met)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1473763NM_001046.3(SLC12A2):c.2210T>A (p.Leu737Gln)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1476334NM_001046.3(SLC12A2):c.1127A>G (p.Asn376Ser)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1505967NM_001046.3(SLC12A2):c.881G>A (p.Arg294His)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1679711NM_001046.3(SLC12A2):c.3566C>T (p.Ala1189Val)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
1679744NM_001046.3(SLC12A2):c.1226T>C (p.Ile409Thr)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
2156078NM_001046.3(SLC12A2):c.376A>T (p.Ser126Cys)SLC12A2Uncertain significancecriteria provided, multiple submitters, no conflicts
3064550NM_001046.3(SLC12A2):c.2756T>C (p.Val919Ala)SLC12A2Uncertain significancecriteria provided, single submitter
3065515NM_001046.3(SLC12A2):c.2361T>G (p.Phe787Leu)SLC12A2Uncertain significancecriteria provided, single submitter
3892444NM_001046.3(SLC12A2):c.2888A>G (p.Asp963Gly)SLC12A2Uncertain significancecriteria provided, single submitter
3892445NM_001046.3(SLC12A2):c.3131C>T (p.Thr1044Met)SLC12A2Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 8 · Orphanet: 2 · 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
SLC12A2StrongAutosomal recessiveKilquist syndrome8

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SLC12A2Orphanet:633021SLC12A2-related autosomal recessive neonatal-developmental delay-intellectual disability-feeding difficulty-sensorineural deafness syndrome
SLC12A2Orphanet:633024SLC12A2-related autosomal dominant infantile-developmental delay-intellectual disability-sensorineural deafness syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SLC12A2HGNC:10911ENSG00000064651P55011Solute carrier family 12 member 2gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SLC12A2Solute carrier family 12 member 2Cation-chloride cotransporter which mediates the electroneutral transport of chloride, potassium and/or sodium ions across the membrane.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

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
Other/Unknown11.8×0.558

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SLC12A2Other/UnknownnoSLC12A1/SLC12A2, NKCC1, AA-permease/SLC12A_dom

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
inferior vagus X ganglion1
palpebral conjunctiva1
parotid gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SLC12A2277ubiquitousmarkerpalpebral conjunctiva, parotid gland, inferior vagus X ganglion

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SLC12A22,461

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
SLC12A2P5501114

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 4. 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
Cation-coupled Chloride cotransporters11631.4×0.002SLC12A2
R-HSA-4253931129.8×0.015SLC12A2
SLC-mediated transmembrane transport159.2×0.023SLC12A2
Transport of small molecules125.1×0.040SLC12A2

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 cell volume116852.0×7e-04SLC12A2
inorganic anion import across plasma membrane18426.0×7e-04SLC12A2
inorganic cation import across plasma membrane18426.0×7e-04SLC12A2
positive regulation of aspartate secretion18426.0×7e-04SLC12A2
regulation of matrix metallopeptidase secretion18426.0×7e-04SLC12A2
regulation of spontaneous synaptic transmission14213.0×0.001SLC12A2
negative regulation of vascular wound healing13370.4×0.001SLC12A2
transepithelial ammonium transport13370.4×0.001SLC12A2
transepithelial chloride transport11872.4×0.001SLC12A2
ammonium transmembrane transport11872.4×0.001SLC12A2
hyperosmotic response11685.2×0.001SLC12A2
intracellular chloride ion homeostasis11685.2×0.001SLC12A2
chloride ion homeostasis11532.0×0.001SLC12A2
T cell chemotaxis11123.5×0.002SLC12A2
cellular response to potassium ion11053.2×0.002SLC12A2
intracellular potassium ion homeostasis1991.3×0.002SLC12A2
cellular response to chemokine1991.3×0.002SLC12A2
sodium ion homeostasis1936.2×0.002SLC12A2
intracellular sodium ion homeostasis1766.0×0.002SLC12A2
potassium ion homeostasis1766.0×0.002SLC12A2
sodium ion import across plasma membrane1624.1×0.002SLC12A2
cell volume homeostasis1601.9×0.002SLC12A2
gamma-aminobutyric acid signaling pathway1543.6×0.002SLC12A2
maintenance of blood-brain barrier1481.5×0.003SLC12A2
potassium ion import across plasma membrane1366.4×0.003SLC12A2
chloride transmembrane transport1237.3×0.005SLC12A2
sodium ion transmembrane transport1203.0×0.005SLC12A2
transport across blood-brain barrier1179.3×0.006SLC12A2
monoatomic ion transport1156.0×0.006SLC12A2

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
SLC12A2BUMETANIDE

Top cohort targets by molecule count

SymbolMoleculesMax phase
SLC12A214

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BUMETANIDE4SLC12A2

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
SLC12A213Binding:9, Functional:4

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

1 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)
BUMETANIDE4SLC12A2

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1SLC12A2
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.