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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
NALCN
sodium leak channel, non-selective
Chromosome 13 Β· 13q32.3-q33.1
NCBI Gene: 259232Ensembl: ENSG00000102452.18HGNC: HGNC:19082UniProt: A0A6Q8PF19
58PubMed Papers
22Diseases
0Drugs
179Pathogenic Variants
FUNCTIONAL ROLE
Ion ChannelTransporter
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
regulation of neuronal action potentialvoltage-gated sodium channel activityplasma membranesodium ion transmembrane transportcongenital contractures of the limbs and face, hypotonia, and developmental delayhypotonia, infantile, with psychomotor retardation and characteristic facies 1hypotonia, infantile, with psychomotor retardation and characteristic faciesgenetic disorder
✦AI Summary

NALCN (sodium leak channel, non-selective) is a voltage-sensing, pore-forming subunit of the NALCN channelosome complex that regulates neuronal excitability through constitutive sodium leak currents 1. The channelosome comprises NALCN, UNC79, UNC80, and FAM155A, with UNC79 and UNC80 forming a HEAT-repeat superhelical assembly that docks onto the NALCN-FAM155A pore complex 1. NALCN controls resting membrane potential and modulates critical physiological processes including respiratory rhythm, circadian regulation, and sensory function 2. The channel conducts monovalent cations while being blocked by physiological extracellular divalent cations and can be activated by neuropeptides like neurotensin via SRC family kinases 3. Genetic variants cause distinct neurodevelopmental syndromes: gain-of-function NALCN mutations cause congenital contractures, hypotonia, and developmental delay (CLIFAHDD), while biallelic loss-of-function variants cause infantile hypotonia with psychomotor retardation (IHPRF1) 3. Loss-of-function variants are associated with severe phenotypes including failure to thrive, central sleep apnea, and refractory epilepsy 3. UNC79 loss-of-function variants also cause neurodevelopmental disorders with intellectual disability, developmental delay, and seizures 4. Beyond neurological function, NALCN regulates epithelial cell shedding and metastatic potential in cancer, with loss-of-function mutations enriched in gastric and colorectal cancers 5.

Sources cited
1
NALCN is the pore-forming subunit of the channelosome complex containing UNC79, UNC80, and FAM155A; regulates resting membrane potential through Na+ leak currents
PMID: 34929720
2
NALCN mediates Na+ leak current regulating resting membrane potential and is involved in respiratory rhythm and sensation
PMID: 38273833
3
Gain-of-function NALCN variants cause CLIFAHDD syndrome; loss-of-function variants cause IHPRF1; loss-of-function associated with failure to thrive, central sleep apnea, and refractory epilepsy
PMID: 40048676
4
UNC79 loss-of-function variants cause neurodevelopmental disorder with intellectual disability, developmental delay, and seizures
PMID: 37183800
5
NALCN regulates epithelial cell shedding and metastasis; loss-of-function mutations enriched in gastric and colorectal cancers
PMID: 36175792
Disease Associationsβ“˜22
congenital contractures of the limbs and face, hypotonia, and developmental delayOpen Targets
0.82Strong
hypotonia, infantile, with psychomotor retardation and characteristic facies 1Open Targets
0.78Strong
hypotonia, infantile, with psychomotor retardation and characteristic faciesOpen Targets
0.57Moderate
genetic disorderOpen Targets
0.54Moderate
Abnormality of the nervous systemOpen Targets
0.44Moderate
Intellectual disabilityOpen Targets
0.39Weak
digitotalar dysmorphismOpen Targets
0.37Weak
Freeman-Sheldon syndromeOpen Targets
0.37Weak
Sheldon-hall syndromeOpen Targets
0.37Weak
arthrogryposis multiplex congenitaOpen Targets
0.36Weak
fetal akinesia deformation sequenceOpen Targets
0.36Weak
fetal akinesia deformation sequence 1Open Targets
0.36Weak
Neurodevelopmental disorderOpen Targets
0.34Weak
CachexiaOpen Targets
0.34Weak
StrabismusOpen Targets
0.34Weak
Abnormal pattern of respirationOpen Targets
0.34Weak
arthrogryposis syndromeOpen Targets
0.34Weak
SeizureOpen Targets
0.34Weak
Severe intellectual disabilityOpen Targets
0.34Weak
autism spectrum disorderOpen Targets
0.33Weak
Congenital contractures of the limbs and face, hypotonia, and developmental delayUniProt
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1UniProt
Pathogenic Variants179
NM_052867.4(NALCN):c.3448C>A (p.Leu1150Ile)Pathogenic
Congenital contractures of the limbs and face, hypotonia, and developmental delay|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 1150
NM_052867.4(NALCN):c.3448C>G (p.Leu1150Val)Pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2026β†’ Residue 1150
NM_052867.4(NALCN):c.518G>C (p.Arg173Pro)Pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 173
NM_052867.4(NALCN):c.3970C>T (p.Leu1324Phe)Pathogenic
Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 1324
NM_052867.4(NALCN):c.3345A>C (p.Lys1115Asn)Likely pathogenic
Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 1115
NM_052867.4(NALCN):c.3058G>A (p.Val1020Ile)Pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 1020
NM_052867.4(NALCN):c.3983T>G (p.Val1328Gly)Likely pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 1328
NM_052867.4(NALCN):c.3553G>A (p.Ala1185Thr)Pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 1185
NM_052867.4(NALCN):c.1497A>G (p.Ile499Met)Likely pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 499
NM_052867.4(NALCN):c.3542G>A (p.Arg1181Gln)Pathogenic
Intellectual disability with episodic ataxia and congenital arthrogryposis|Congenital contractures of the limbs and face, hypotonia, and developmental delay|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 1181
NM_052867.4(NALCN):c.986G>C (p.Arg329Thr)Likely pathogenic
Inborn genetic diseases|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 329
NM_052867.4(NALCN):c.1550T>G (p.Leu517Trp)Likely pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 517
NM_052867.4(NALCN):c.965T>C (p.Ile322Thr)Pathogenic
Congenital contractures of the limbs and face, hypotonia, and developmental delay|not provided|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 322
NM_052867.4(NALCN):c.985A>G (p.Arg329Gly)Pathogenic
not provided|Congenital contractures of the limbs and face, hypotonia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 329
NM_052867.4(NALCN):c.2563C>T (p.Arg855Ter)Pathogenic
not provided|Inborn genetic diseases|Hypotonia, infantile, with psychomotor retardation and characteristic facies 1|NALCN-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 855
NM_052867.4(NALCN):c.2524C>T (p.Arg842Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 842
NM_052867.4(NALCN):c.454C>T (p.Arg152Ter)Pathogenic
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1|Congenital contractures of the limbs and face, hypotonia, and developmental delay|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 152
NM_052867.4(NALCN):c.1745A>G (p.Tyr582Cys)Pathogenic
not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 582
NM_052867.4(NALCN):c.1245C>A (p.Tyr415Ter)Pathogenic
NALCN-related disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 415
NM_052867.4(NALCN):c.3056dup (p.Leu1019fs)Pathogenic
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1|not provided|not specified
β˜…β˜…β˜†β˜†2024β†’ Residue 1019
View on ClinVar β†—
Related Genes
CALM3Protein interaction94%CALM2Protein interaction93%TACR1Protein interaction87%NTSProtein interaction84%TAC1Protein interaction83%C2CD4AProtein interaction72%
Tissue Expression6 tissues
Brain
100%
Heart
37%
Ovary
8%
Liver
4%
Lung
4%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
NALCNCALM3CALM2TACR1NTSTAC1C2CD4A
PROTEIN STRUCTURE
Preparing viewer…
PDB6XIW Β· 2.80 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.58Moderately Constrained
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.49 [0.42–0.58]
RankingsWhere NALCN stands among ~20K protein-coding genes
  • #7,895of 20,598
    Most Researched58
  • #402of 5,498
    Most Pathogenic Variants179 Β· top 10%
  • #3,857of 17,882
    Most Constrained (LOEUF)0.58 Β· top quartile
Genes detectedNALCN
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
A new neurodevelopmental disorder linked to heterozygous variants in UNC79.
PMID: 37183800
Genet Med Β· 2023
1.00
2
A 20-year Clinical and Genetic Neuromuscular Cohort Analysis in Lebanon: An International Effort.
PMID: 34602496
J Neuromuscul Dis Β· 2022
0.90
3
Genotype-Phenotype Landscape of
PMID: 40048676
Neurology Β· 2025
0.80
4
The NALCN channel regulates metastasis and nonmalignant cell dissemination.
PMID: 36175792
Nat Genet Β· 2022
0.70
5
Structural architecture of the human NALCN channelosome.
PMID: 34929720
Nature Β· 2022
0.60