Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	259232
Gene name	Sodium leak channel, non-selective
Gene symbol	NALCN
Synonyms (NCBI Gene)	CLIFAHDDCanIonIHPRFIHPRF1INNFDVGCNL1bA430M15.1
Chromosome	13
Chromosome location	13q32.3-q33.1
Summary	This gene encodes a voltage-independent, nonselective cation channel which belongs to a family of voltage-gated sodium and calcium channels that regulates the resting membrane potential and excitability of neurons. This family is expressed throughout the

Show/Hide all (66)

SNP ID	Visualize variation	Clinical significance	Consequence
rs201402954	C>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs376152742	G>A	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs527789070	A>C,G	Pathogenic	Synonymous variant, coding sequence variant, genic upstream transcript variant, stop gained
rs587777038	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs587777068	C>A	Pathogenic	Missense variant, coding sequence variant
rs757674263	G>A	Pathogenic	Stop gained, coding sequence variant
rs762389271	T>C	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs763237578	C>G,T	Likely-pathogenic	Intron variant
rs766421214	G>A	Pathogenic	Stop gained, coding sequence variant
rs771015295	G>A,C	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, stop gained
rs772394714	A>-,AA	Pathogenic	Frameshift variant, coding sequence variant
rs786201003	C>T	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant
rs786203984	T>G	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant
rs786203985	A>C	Pathogenic	Coding sequence variant, missense variant
rs786203986	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs786203987	A>G	Pathogenic	Coding sequence variant, missense variant
rs786203988	T>C,G	Pathogenic	Coding sequence variant, missense variant
rs869025188	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs869312873	C>T	Pathogenic	Coding sequence variant, synonymous variant
rs869312952	C>G,T	Pathogenic	Splice donor variant
rs878853127	A>C	Pathogenic	Coding sequence variant, missense variant
rs878853128	T>G	Pathogenic	Coding sequence variant, missense variant
rs878853129	A>G	Pathogenic	Coding sequence variant, missense variant
rs878853130	A>G	Pathogenic	Coding sequence variant, missense variant
rs878853131	G>T	Pathogenic	Coding sequence variant, missense variant
rs878853132	A>C	Pathogenic	Coding sequence variant, missense variant
rs878853133	C>T	Pathogenic	Coding sequence variant, missense variant
rs878853134	G>T	Pathogenic	Coding sequence variant, missense variant
rs972964381	G>A	Pathogenic	Coding sequence variant, stop gained
rs1031314447	G>A	Pathogenic	Coding sequence variant, stop gained
rs1057516040	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1057519432	T>C	Pathogenic	Coding sequence variant, missense variant
rs1057519433	A>G	Pathogenic	Coding sequence variant, missense variant
rs1064794722	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1064795423	A>C	Pathogenic	Coding sequence variant, missense variant
rs1064796154	CT>-	Pathogenic	Coding sequence variant, frameshift variant
rs1158141270	C>A	Likely-pathogenic	Splice donor variant
rs1158771233	G>T	Pathogenic	Coding sequence variant, stop gained
rs1255534617	->A	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs1333710212	T>C	Pathogenic	Splice acceptor variant
rs1459166839	T>A,C	Pathogenic	Coding sequence variant, missense variant
rs1555309004	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1555373511	C>G	Likely-pathogenic	Splice acceptor variant
rs1555375944	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1555378616	G>C,T	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs1555379886	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1555381108	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1555383003	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1566385468	G>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1566460907	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1566815386	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1594134160	G>T	Pathogenic	Coding sequence variant, missense variant
rs1594146891	A>G	Pathogenic	Splice donor variant
rs1594168638	G>A	Pathogenic	Stop gained, coding sequence variant
rs1594168705	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1594211051	TTAC>-	Pathogenic	Splice donor variant, intron variant
rs1594211244	->A	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1594211334	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1594211911	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1594212468	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1594218864	->T	Pathogenic	Coding sequence variant, frameshift variant
rs1594368726	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1594368753	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1594616249	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1594759803	C>-	Pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant
rs1594761911	C>T	Pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant

Show/Hide all (27)

miRTarBase ID	miRNA	Experiments	Reference
MIRT023347	hsa-miR-122-5p	Microarray	17612493
MIRT1173192	hsa-miR-1200	CLIP-seq
MIRT1173193	hsa-miR-1254	CLIP-seq
MIRT1173194	hsa-miR-1278	CLIP-seq
MIRT1173195	hsa-miR-1537	CLIP-seq
MIRT1173196	hsa-miR-2054	CLIP-seq
MIRT1173197	hsa-miR-300	CLIP-seq
MIRT1173198	hsa-miR-3116	CLIP-seq
MIRT1173199	hsa-miR-381	CLIP-seq
MIRT1173200	hsa-miR-3907	CLIP-seq
MIRT1173201	hsa-miR-4282	CLIP-seq
MIRT1173202	hsa-miR-4324	CLIP-seq
MIRT1173203	hsa-miR-4327	CLIP-seq
MIRT1173204	hsa-miR-4528	CLIP-seq
MIRT1173205	hsa-miR-4666-3p	CLIP-seq
MIRT1173206	hsa-miR-4789-5p	CLIP-seq
MIRT1173207	hsa-miR-4793-5p	CLIP-seq
MIRT1173208	hsa-miR-544b	CLIP-seq
MIRT1173209	hsa-miR-548q	CLIP-seq
MIRT1173210	hsa-miR-616	CLIP-seq
MIRT1173211	hsa-miR-636	CLIP-seq
MIRT1173212	hsa-miR-661	CLIP-seq
MIRT2050200	hsa-miR-129-5p	CLIP-seq
MIRT2050200	hsa-miR-129-5p	CLIP-seq
MIRT1173196	hsa-miR-2054	CLIP-seq
MIRT2279099	hsa-miR-3908	CLIP-seq
MIRT1173201	hsa-miR-4282	CLIP-seq

Show/Hide all (28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005248	Function	Voltage-gated sodium channel activity	IDA	32698188
GO:0005248	Function	Voltage-gated sodium channel activity	IMP	32494638
GO:0005261	Function	Monoatomic cation channel activity	IBA
GO:0005261	Function	Monoatomic cation channel activity	IEA
GO:0005261	Function	Monoatomic cation channel activity	ISS
GO:0005272	Function	Sodium channel activity	IEA
GO:0005272	Function	Sodium channel activity	TAS
GO:0005515	Function	Protein binding	IPI	19575010, 25416956
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IDA	31409833, 32698188
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006814	Process	Sodium ion transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0022840	Function	Leak channel activity	ISS
GO:0032224	Process	Positive regulation of synaptic transmission, cholinergic	IBA
GO:0032230	Process	Positive regulation of synaptic transmission, GABAergic	IBA
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	TAS
GO:0034702	Component	Monoatomic ion channel complex	IEA
GO:0035725	Process	Sodium ion transmembrane transport	IEA
GO:0035725	Process	Sodium ion transmembrane transport	ISS
GO:0055085	Process	Transmembrane transport	IEA
GO:0060075	Process	Regulation of resting membrane potential	ISS
GO:0070588	Process	Calcium ion transmembrane transport	ISS
GO:0071805	Process	Potassium ion transmembrane transport	ISS

MIM	HGNC	e!Ensembl
611549	19082	ENSG00000102452

Q8IZF0

Protein name

Sodium leak channel NALCN (CanIon) (Sodium leak channel non-selective protein) (Voltage gated channel-like protein 1)

Protein function

Voltage-gated ion channel responsible for the resting Na(+) permeability that controls neuronal excitability (PubMed:17448995, PubMed:31409833). NALCN channel functions as a multi-protein complex, which consists at least of NALCN, NALF1, UNC79 a

PDB

6XIW , 7CM3 , 7SX3 , 7SX4 , 7WJI

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00520	Ion_trans	35 → 333	Ion transport protein	Family
PF00520	Ion_trans	383 → 609	Ion transport protein	Family
PF00520	Ion_trans	885 → 1166	Ion transport protein	Family
PF00520	Ion_trans	1209 → 1458	Ion transport protein	Family

Sequence

MLKRKQSSRVEAQPVTDFGPDESLSDNADILWINKPWVHSLLRICAIISVISVCMNTPMT
FEHYPPLQYVTFTLDTLLMFLYTAEMIAKMHIRGIVKGDSSYVKDRWCVFDGFMVFCLWV
SLVLQVFEIADIVDQMSPWGMLRIPRPLIMIRAFRIYFRFELPRTRITNILKRSGEQIWS
VSIFLLFFLLLYGILGVQMFGTFTYHCVVNDTKPGNVTWNSLAIPDTHCSPELEEGYQCP
PGFKCMDLEDLGLSRQELGYSGFNEIGTSIFTVYEAASQEGWVFLMYRAIDSFPRWRSYF
YFITLIFFLAWLVKNVFIAVIIETFAEIRVQFQQMWGSRSSTTSTATTQMFHEDAAGGWQ
LVAVDVNKPQGRAPACLQKMMRSSVFHMFILSMVTVDVIVAASNYYKGENFRRQYDEFYL
AEVAFTVLFDLEALLKIWCLGFTGYISSSLHKFELLLVIGTTLHVYPDLYHSQFTYFQVL
RVVRLIKISPALEDFVYKIFGPGKKLGSLVVFTASLLIVMSAISLQMFCFVEELDRFTTF
PRAFMSMFQILTQEGWVDVMDQTLNAVGHMWAPVVAIYFILYHLFATLILLSLFVAVILD
NLELDEDLKKLKQLKQSEANADTKEKLPLRLRIFEKFPNRPQMVKISKLPSDFTVPKIRE
SFMKQFIDRQQQDTCCLLRSLPTTSSSSCDHSKRSAIEDNKYIDQKLRKSVFSIRARNLL
EKETAVTKILRACTRQRMLSGSFEGQPAKERSILSVQHHIRQERRSLRHGSNSQRISRGK
SLETLTQDHSNTVRYRNAQREDSEIKMIQEKKEQAEMKRKVQEEELRENHPYFDKPLFIV
GREHRFRNFCRVVVRARFNASKTDPVTGAVKNTKYHQLYDLLGLVTYLDWVMIIVTICSC
ISMMFESPFRRVMHAPTLQIAEYVFVIFMSIELNLKIMADGLFFTPTAVIRDFGGVMDIF
IYLVSLIFLCWMPQNVPAESGAQLLMVLRCLRPLRIFKLVPQMRKVVRELFSGFKEIFLV
SILLLTLMLVFASFGVQLFAGKLAKCNDPNIIRREDCNGIFRINVSVSKNLNLKLRPGEK
KPGFWVPRVWANPRNFNFDNVGNAMLALFEVLSLKGWVEVRDVIIHRVGPIHGIYIHVFV
FLGCMIGLTLFVGVVIANFNENKGTALLTVDQRRWEDLKSRLKIAQPLHLPPRPDNDGFR
AKMYDITQHPFFKRTIALLVLAQSVLLSVKWDVEDPVTVPLATMSVVFTFIFVLEVTMKI
IAMSPAGFWQSRRNRYDLLVTSLGVVWVVLHFALLNAYTYMMGACVIVFRFFSICGKHVT
LKMLLLTVVVSMYKSFFIIVGMFLLLLCYAFAGVVLFGTVKYGENINRHANFSSAGKAIT
VLFRIVTGEDWNKIMHDCMVQPPFCTPDEFTYWATDCGNYAGALMYFCSFYVIIAYIMLN
LLVAIIVENFSLFYSTEEDQLLSYNDLRHFQIIWNMVDDKREGVIPTFRVKFLLRLLRGR
LEVDLDKDKLLFKHMCYEMERLHNGGDVTFHDVLSMLSYRSVDIRKSLQLEELLAREQLE
YTIEEEVAKQTIRMWLKKCLKRIRAKQQQSCSIIHSLRESQQQELSRFLNPPSIETTQPS
EDTNANSQDNSMQPETSSQQQLLSPTLSDRGGSRQDAADAGKPQRKFGQWRLPSAPKPIS
HSVSSVNLRFGGRTTMKSVVCKMNPMTDAASCGSEVKKWWTRQLTVESDESGDDLLDI

Sequence length

1738

Interactions

View interactions

	Reactome
			Stimuli-sensing channels

292

Show/Hide Causal Diseases (16)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal pattern of respiration	Pathogenic	rs869312873	RCV000210426
Abnormality of the nervous system	Likely pathogenic; Pathogenic	rs2140132954, rs2140156819, rs2041614157	RCV001814522 RCV001814347 RCV001814276
Arthrogryposis multiplex congenita	Likely pathogenic	rs1594368753, rs1594616249, rs762389271	RCV000855468 RCV000855467 RCV000855469
Arthrogryposis syndrome	Likely pathogenic; Pathogenic	rs786203988	RCV005625484
Cachexia	Pathogenic	rs869312873	RCV000210426
Congenital contractures of the limbs and face, hypotonia, and developmental delay	Likely pathogenic; Pathogenic	rs2139938444, rs2139420897, rs2139514134, rs541633673, rs2139519168, rs774096141, rs2139938691, rs878853129, rs786203984, rs786203985, rs786203986, rs786203987, rs786203988, rs786201003, rs2502043267 View all (24 more)	RCV001868410 RCV001725863 RCV001775426 RCV002478009 RCV002250800 RCV003235691 RCV002271994 RCV003159077 RCV000167528 RCV000167529 RCV000167530 RCV000167531 RCV000167532 RCV000224736 RCV002468750 RCV003234204 RCV003984831 RCV000224385 RCV000224193 RCV000224534 RCV000224757 RCV000224900 RCV000224242 RCV000224921 RCV000224612 RCV001254037 RCV003493341 RCV004560339 RCV004586434 RCV000408614 RCV000416437 RCV000416463 RCV000763319 RCV000768409 RCV000768410 RCV003984848 RCV001252584 RCV000853279 RCV001007895 RCV001250195 RCV002464434
Fetal akinesia deformation sequence 1	Likely pathogenic	rs1594368753, rs1594616249, rs762389271	RCV000855468 RCV000855467 RCV000855469
Hypotonia, infantile, with psychomotor retardation and characteristic facies 1	Likely pathogenic; Pathogenic	rs541633673, rs2139438975, rs774096141, rs2033656475, rs2501833379, rs2502452053, rs2548589416, rs376152742, rs1158141270, rs1158771233, rs1555379886, rs1333710212, rs1459166839, rs1594134160, rs1031314447 View all (18 more)	RCV002478009 RCV002052429 RCV002250917 RCV002255774 RCV002283795 RCV003152549 RCV003338145 RCV001090146 RCV000763319 RCV000625918 RCV000625775 RCV005357875 RCV000845223 RCV000845219 RCV000845225 RCV000845221 RCV000845218 RCV000845216 RCV000845227 RCV000845217 RCV000845222 RCV000845228 RCV000845226 RCV000845220 RCV000845224 RCV000055644 RCV000985067 RCV000985052 RCV001004862 RCV001169972 RCV000074369 RCV000074370 RCV001291687
Intellectual disability	Pathogenic	rs2139465605	RCV001526696
Intellectual disability with episodic ataxia and congenital arthrogryposis	Likely pathogenic; Pathogenic	rs786201003	RCV000167764
NALCN-related disorder	Likely pathogenic; Pathogenic	rs878853129, rs1426944195, rs1308457240, rs376152742, rs1031314447, rs1594368726	RCV004534040 RCV003335867 RCV004529761 RCV005250079 RCV003336223 RCV004538169
Neurodevelopmental disorder	Pathogenic	rs2139408863	RCV001780032
See cases	Likely pathogenic; Pathogenic	rs541633673, rs2139795638	RCV002252705 RCV002252375
Seizure	Pathogenic	rs869312873	RCV000210426
Severe intellectual disability	Pathogenic	rs869312873	RCV000210426
Strabismus	Pathogenic	rs869312873	RCV000210426

Show/Hide Unknown Diseases (11)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autism spectrum disorder	Conflicting classifications of pathogenicity; association	rs755839325, rs2045687348	RCV003127466 RCV001291264
Cholangiocarcinoma	Benign	rs10508056, rs554997	RCV005915147 RCV005925301
Developmental disorder	Conflicting classifications of pathogenicity	rs2033130135	RCV003127467
Gastric cancer	Likely benign	rs17581591	RCV005919299
Hypotonia, infantile, with psychomotor retardation and characteristic facies	Uncertain significance	rs1198648713	RCV002466936
Lung cancer	Benign	rs10508056	RCV005915148
Malignant lymphoma, large B-cell, diffuse	Benign	rs10508056	RCV005915146
Malignant tumor of esophagus	Benign; Likely benign	rs150580612	RCV005907055
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs16958350, rs150580612	RCV005894274 RCV005907056
Sarcoma	Likely benign	rs17581591	RCV005919298
Uterine carcinosarcoma	Benign	rs4322520	RCV005924801

Show/Hide Text Mining Associations (37)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	33797837
Apnea	Associate	29610177
Arthrogryposis multiplex congenita distal type 1	Associate	25683120
Bipolar Disorder	Associate	24075186
Blast Crisis	Associate	33557955
Carcinoma Non Small Cell Lung	Associate	39766220
Cerebral Palsy	Associate	33557955
Channelopathies	Associate	30167850
Cognition Disorders	Associate	24075186, 29610177
Constipation	Associate	24075186
Contracture	Associate	25683120, 30167850, 31409833, 35055596
COVID 19	Associate	36104591
Death	Associate	29610177
Developmental Disabilities	Associate	25683120, 30167850, 31409833, 35055596
Disease	Associate	30167850
Dystonia	Associate	24227479, 33557955
Endometriosis	Associate	37789421
Facial Dysmorphism with Multiple Malformations	Associate	24075186, 29610177
Freeman Sheldon syndrome	Associate	25683120
Genetic Diseases Inborn	Associate	24075186
Heart Defects Congenital	Associate	34324492
Infantile Epileptic Dyskinetic Encephalopathy	Associate	26708753
Intellectual Disability	Associate	24075186, 25683120, 31409833, 35055596
Language Development Disorders	Associate	29610177
Motor Neuron Disease	Associate	33557955
Muscle Hypotonia	Associate	24075186, 25683120, 29610177, 30167850, 31409833, 35055596
Neoplasms	Inhibit	39766220
Neuroaxonal Dystrophies	Associate	29610177
Pathological Conditions Anatomical	Associate	25683120
Psychomotor Disorders	Associate	30167850
Respiratory Insufficiency	Associate	29610177
Retinitis Pigmentosa	Inhibit	27297950
Schizophrenia	Associate	24075186
Seizures	Associate	33557955
Sleep Apnea Central	Associate	29610177
Sleep Apnea Syndromes	Associate	29610177
Speech Disorders	Associate	24075186, 29610177

NALCN (sodium leak channel, non-selective)