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	1183
Gene name	Chloride voltage-gated channel 4
Gene symbol	CLCN4
Synonyms (NCBI Gene)	CLC4ClC-4ClC-4AMRX15MRX49MRXSRC
Chromosome	X
Chromosome location	Xp22.2
Summary	The CLCN family of voltage-dependent chloride channel genes comprises nine members (CLCN1-7, Ka and Kb) which demonstrate quite diverse functional characteristics while sharing significant sequence homology. Chloride channel 4 has an evolutionary conserve

Show/Hide all (23)

SNP ID	Visualize variation	Clinical significance	Consequence
rs483352716	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs587777161	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs879255580	T>G	Pathogenic	Missense variant, coding sequence variant
rs879255581	T>C	Pathogenic	Missense variant, coding sequence variant
rs879255582	C>T	Pathogenic	Missense variant, coding sequence variant
rs879255583	C>T	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs879255584	C>T	Pathogenic	Missense variant, coding sequence variant
rs879255585	G>A,C	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs879255586	->A	Pathogenic	Frameshift variant, coding sequence variant
rs879255590	G>A	Uncertain-significance, pathogenic	Intron variant
rs879255591	G>A	Uncertain-significance, likely-pathogenic	Intron variant, missense variant, coding sequence variant
rs1131691687	G>A	Likely-pathogenic, not-provided	Missense variant, coding sequence variant
rs1246068842	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1555973635	A>G	Likely-pathogenic	Intron variant, missense variant, initiator codon variant
rs1555976161	T>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1555976933	C>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1555976973	G>A	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs1555977164	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1569226551	G>A	Pathogenic	Coding sequence variant, missense variant, intron variant
rs1569230006	C>G	Pathogenic	Coding sequence variant, missense variant
rs1569231897	G>A	Pathogenic	Coding sequence variant, missense variant
rs1569233549	G>C	Pathogenic	Coding sequence variant, missense variant
rs1602159841	G>A	Likely-pathogenic	Coding sequence variant, missense variant

149

Show/Hide all (149)

miRTarBase ID	miRNA	Experiments
MIRT894574	hsa-miR-1252	CLIP-seq
MIRT894575	hsa-miR-1260	CLIP-seq
MIRT894576	hsa-miR-1260b	CLIP-seq
MIRT894577	hsa-miR-1276	CLIP-seq
MIRT894578	hsa-miR-1283	CLIP-seq
MIRT894579	hsa-miR-145	CLIP-seq
MIRT894580	hsa-miR-188-3p	CLIP-seq
MIRT894581	hsa-miR-300	CLIP-seq
MIRT894582	hsa-miR-3156-3p	CLIP-seq
MIRT894583	hsa-miR-3163	CLIP-seq
MIRT894584	hsa-miR-3168	CLIP-seq
MIRT894585	hsa-miR-3176	CLIP-seq
MIRT894586	hsa-miR-3202	CLIP-seq
MIRT894587	hsa-miR-320a	CLIP-seq
MIRT894588	hsa-miR-320b	CLIP-seq
MIRT894589	hsa-miR-320c	CLIP-seq
MIRT894590	hsa-miR-320d	CLIP-seq
MIRT894591	hsa-miR-3662	CLIP-seq
MIRT894592	hsa-miR-3667-3p	CLIP-seq
MIRT894593	hsa-miR-371b-5p	CLIP-seq
MIRT894594	hsa-miR-381	CLIP-seq
MIRT894595	hsa-miR-3922-3p	CLIP-seq
MIRT894596	hsa-miR-3942-5p	CLIP-seq
MIRT894597	hsa-miR-4276	CLIP-seq
MIRT894598	hsa-miR-4302	CLIP-seq
MIRT894599	hsa-miR-4311	CLIP-seq
MIRT894600	hsa-miR-4328	CLIP-seq
MIRT894601	hsa-miR-4429	CLIP-seq
MIRT894602	hsa-miR-4533	CLIP-seq
MIRT894603	hsa-miR-4540	CLIP-seq
MIRT894604	hsa-miR-4652-3p	CLIP-seq
MIRT894605	hsa-miR-4654	CLIP-seq
MIRT894606	hsa-miR-4698	CLIP-seq
MIRT894607	hsa-miR-4703-5p	CLIP-seq
MIRT894608	hsa-miR-4731-5p	CLIP-seq
MIRT894609	hsa-miR-4744	CLIP-seq
MIRT894610	hsa-miR-4769-5p	CLIP-seq
MIRT894611	hsa-miR-499a-5p	CLIP-seq
MIRT894612	hsa-miR-583	CLIP-seq
MIRT894613	hsa-miR-617	CLIP-seq
MIRT894614	hsa-miR-629	CLIP-seq
MIRT1965303	hsa-miR-1208	CLIP-seq
MIRT1965304	hsa-miR-132	CLIP-seq
MIRT1965305	hsa-miR-194	CLIP-seq
MIRT1965306	hsa-miR-204	CLIP-seq
MIRT1965307	hsa-miR-211	CLIP-seq
MIRT1965308	hsa-miR-212	CLIP-seq
MIRT1965309	hsa-miR-3591-3p	CLIP-seq
MIRT1965310	hsa-miR-3924	CLIP-seq
MIRT1965311	hsa-miR-4254	CLIP-seq
MIRT1965312	hsa-miR-4427	CLIP-seq
MIRT1965313	hsa-miR-4434	CLIP-seq
MIRT1965314	hsa-miR-4516	CLIP-seq
MIRT1965315	hsa-miR-452	CLIP-seq
MIRT1965316	hsa-miR-4531	CLIP-seq
MIRT1965317	hsa-miR-4676-3p	CLIP-seq
MIRT1965318	hsa-miR-4755-5p	CLIP-seq
MIRT1965319	hsa-miR-4793-5p	CLIP-seq
MIRT1965320	hsa-miR-490-3p	CLIP-seq
MIRT1965321	hsa-miR-548a-5p	CLIP-seq
MIRT1965322	hsa-miR-548ab	CLIP-seq
MIRT1965323	hsa-miR-548ak	CLIP-seq
MIRT1965324	hsa-miR-548b-5p	CLIP-seq
MIRT1965325	hsa-miR-548c-5p	CLIP-seq
MIRT1965326	hsa-miR-548d-5p	CLIP-seq
MIRT1965327	hsa-miR-548h	CLIP-seq
MIRT1965328	hsa-miR-548i	CLIP-seq
MIRT1965329	hsa-miR-548j	CLIP-seq
MIRT1965330	hsa-miR-548m	CLIP-seq
MIRT1965331	hsa-miR-548w	CLIP-seq
MIRT1965332	hsa-miR-548y	CLIP-seq
MIRT1965333	hsa-miR-559	CLIP-seq
MIRT1965334	hsa-miR-619	CLIP-seq
MIRT1965335	hsa-miR-623	CLIP-seq
MIRT1965336	hsa-miR-649	CLIP-seq
MIRT1965337	hsa-miR-802	CLIP-seq
MIRT2201271	hsa-miR-1323	CLIP-seq
MIRT2201272	hsa-miR-15a	CLIP-seq
MIRT2201273	hsa-miR-15b	CLIP-seq
MIRT2201274	hsa-miR-16	CLIP-seq
MIRT2201275	hsa-miR-195	CLIP-seq
MIRT894584	hsa-miR-3168	CLIP-seq
MIRT894593	hsa-miR-371b-5p	CLIP-seq
MIRT2201276	hsa-miR-424	CLIP-seq
MIRT894597	hsa-miR-4276	CLIP-seq
MIRT894598	hsa-miR-4302	CLIP-seq
MIRT2201277	hsa-miR-4524	CLIP-seq
MIRT894606	hsa-miR-4698	CLIP-seq
MIRT894608	hsa-miR-4731-5p	CLIP-seq
MIRT1965319	hsa-miR-4793-5p	CLIP-seq
MIRT2201278	hsa-miR-4803	CLIP-seq
MIRT2201279	hsa-miR-496	CLIP-seq
MIRT2201280	hsa-miR-497	CLIP-seq
MIRT2201281	hsa-miR-503	CLIP-seq
MIRT2201282	hsa-miR-545	CLIP-seq
MIRT2201283	hsa-miR-548o	CLIP-seq
MIRT2201284	hsa-miR-548p	CLIP-seq
MIRT894614	hsa-miR-629	CLIP-seq
MIRT2201285	hsa-miR-646	CLIP-seq
MIRT1965337	hsa-miR-802	CLIP-seq
MIRT1965311	hsa-miR-4254	CLIP-seq
MIRT2447127	hsa-miR-4282	CLIP-seq
MIRT1965313	hsa-miR-4434	CLIP-seq
MIRT1965314	hsa-miR-4516	CLIP-seq
MIRT1965316	hsa-miR-4531	CLIP-seq
MIRT1965320	hsa-miR-490-3p	CLIP-seq
MIRT2447128	hsa-miR-513a-3p	CLIP-seq
MIRT1965334	hsa-miR-619	CLIP-seq
MIRT1965336	hsa-miR-649	CLIP-seq
MIRT1965303	hsa-miR-1208	CLIP-seq
MIRT2504059	hsa-miR-1269	CLIP-seq
MIRT2504060	hsa-miR-1269b	CLIP-seq
MIRT2504061	hsa-miR-1301	CLIP-seq
MIRT2504062	hsa-miR-1825	CLIP-seq
MIRT2504063	hsa-miR-199a-5p	CLIP-seq
MIRT2504064	hsa-miR-199b-5p	CLIP-seq
MIRT2504065	hsa-miR-3125	CLIP-seq
MIRT2504066	hsa-miR-3148	CLIP-seq
MIRT2504067	hsa-miR-3161	CLIP-seq
MIRT2504068	hsa-miR-3183	CLIP-seq
MIRT2504069	hsa-miR-3200-5p	CLIP-seq
MIRT2504070	hsa-miR-3667-5p	CLIP-seq
MIRT2504071	hsa-miR-3912	CLIP-seq
MIRT2504072	hsa-miR-3916	CLIP-seq
MIRT2504073	hsa-miR-4324	CLIP-seq
MIRT2504074	hsa-miR-4420	CLIP-seq
MIRT2504075	hsa-miR-4504	CLIP-seq
MIRT2504076	hsa-miR-4520b-3p	CLIP-seq
MIRT2504077	hsa-miR-4529-3p	CLIP-seq
MIRT2504078	hsa-miR-4633-5p	CLIP-seq
MIRT2504079	hsa-miR-4660	CLIP-seq
MIRT2504080	hsa-miR-4723-3p	CLIP-seq
MIRT2504081	hsa-miR-4749-3p	CLIP-seq
MIRT1965319	hsa-miR-4793-5p	CLIP-seq
MIRT2504082	hsa-miR-5047	CLIP-seq
MIRT2504083	hsa-miR-511	CLIP-seq
MIRT2504084	hsa-miR-532-5p	CLIP-seq
MIRT2504085	hsa-miR-549	CLIP-seq
MIRT2504086	hsa-miR-562	CLIP-seq
MIRT1965337	hsa-miR-802	CLIP-seq
MIRT2504087	hsa-miR-892a	CLIP-seq
MIRT2504068	hsa-miR-3183	CLIP-seq
MIRT2504070	hsa-miR-3667-5p	CLIP-seq
MIRT2504071	hsa-miR-3912	CLIP-seq
MIRT2504078	hsa-miR-4633-5p	CLIP-seq
MIRT2504080	hsa-miR-4723-3p	CLIP-seq
MIRT1965319	hsa-miR-4793-5p	CLIP-seq
MIRT2504084	hsa-miR-532-5p	CLIP-seq
MIRT2504085	hsa-miR-549	CLIP-seq

Show/Hide all (40)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005247	Function	Voltage-gated chloride channel activity	IBA
GO:0005247	Function	Voltage-gated chloride channel activity	IEA
GO:0005247	Function	Voltage-gated chloride channel activity	TAS	8069296
GO:0005254	Function	Chloride channel activity	IDA	10564087
GO:0005254	Function	Chloride channel activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005524	Function	ATP binding	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	28972156
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IBA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	17023393, 27550844, 28972156
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005794	Component	Golgi apparatus	IBA
GO:0005886	Component	Plasma membrane	IBA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006821	Process	Chloride transport	IDA	10564087
GO:0006821	Process	Chloride transport	IEA
GO:0006821	Process	Chloride transport	IMP	23647072, 25644381
GO:0008021	Component	Synaptic vesicle	IBA
GO:0010008	Component	Endosome membrane	IDA	28972156
GO:0010008	Component	Endosome membrane	TAS
GO:0015108	Function	Chloride transmembrane transporter activity	IEA
GO:0015297	Function	Antiporter activity	IDA	28972156
GO:0015297	Function	Antiporter activity	IEA
GO:0015297	Function	Antiporter activity	IMP	23647072, 27550844
GO:0015297	Function	Antiporter activity	TAS
GO:0016020	Component	Membrane	IEA
GO:0031901	Component	Early endosome membrane	IEA
GO:0031902	Component	Late endosome membrane	IEA
GO:0034220	Process	Monoatomic ion transmembrane transport	TAS
GO:0055037	Component	Recycling endosome	IDA	28972156
GO:0055038	Component	Recycling endosome membrane	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0097546	Component	Ciliary base	IEA
GO:1902476	Process	Chloride transmembrane transport	IEA
GO:1905515	Process	Non-motile cilium assembly	IEA

MIM	HGNC	e!Ensembl
302910	2022	ENSG00000073464

P51793

Protein name

H(+)/Cl(-) exchange transporter 4 (Chloride channel protein 4) (ClC-4) (Chloride transporter ClC-4)

Protein function

Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (PubMed:18063579, PubMed:23647072, PubMed:25644381, PubMed:27550844, PubMed:28972156). The CLC channel family contains b

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00654	Voltage_CLC	162 → 565	Voltage gated chloride channel	Family
PF00571	CBS	596 → 660	CBS domain	Domain
PF00571	CBS	693 → 748	CBS domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Abundant in skeletal muscle and also detectable in brain and heart.

Sequence

MVNAGAMSGSGNLMDFLDEPFPDVGTYEDFHTIDWLREKSRDTDRHRKITSKSKESIWEF
IKSLLDAWSGWVVMLLIGLLAGTLAGVIDLAVDWMTDLKEGVCLSAFWYSHEQCCWTSNE
TTFEDRDKCPLWQKWSELLVNQSEGASAYILNYLMYILWALLFAFLAVSLVRVFAPYACG
SGIPEIKTILSGFIIRGYLGKWTLLIKTVTLVLVVSSGLSLGKEGPLVHVACCCGNFFSS
LFSKYSKNEGKRREVLSAAAAAGVSVAFGAPIGGVLFSLEEVSYYFPLKTLWRSFFAALV
AAFTLRSINPFGNSRLVLFYVEYHTPWYMAELFPFILLGVFGGLWGTLFIRCNIAWCRRR
KTTRLGKYPVLEVIVVTAITAIIAYPNPYTRQSTSELISELFNDCGALESSQLCDYINDP
NMTRPVDDIPDRPAGVGVYTAMWQLALALIFKIVVTIFTFGMKIPSGLFIPSMAVGAIAG
RMVGIGVEQLAYHHHDWIIFRNWCRPGADCVTPGLYAMVGAAACLGGVTRMTVSLVVIMF
ELTGGLEYIVPLMAAAVTSKWVADAFGKEGIYEAHIHLNGYPFLDVKDEFTHRTLATDVM
RPRRGEPPLSVLTQDSMTVEDVETLIKETDYNGFPVVVSRDSERLIGFAQRRELILAIKN
ARQRQEGIVSNSIMYFTEEPPELPANSPHPLKLRRILNLSPFTVTDHTPMETVVDIFRKL
GLRQCLVTRSGRLLGIITKKDVLRHMAQMANQDPESIMFN

Sequence length

760

Interactions

View interactions

	KEGG		Reactome
	Neutrophil extracellular trap formation		Stimuli-sensing channels

170

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
CLCN4-related disorder	Pathogenic; Likely pathogenic	rs879255580, rs879255581, rs879255582, rs879255583, rs879255584, rs879255585, rs879255586, rs587777161, rs1131691687	RCV000239752 RCV000239766 RCV000239736 RCV000239763 RCV000239734 RCV000239756 RCV000239738 RCV000239727 RCV000509195
Intellectual disability	Likely pathogenic; Pathogenic	rs1064796023	RCV001260685
Intellectual disability, X-linked 49	Pathogenic; Likely pathogenic	rs587777161, rs2147179499, rs2147178526, rs2147167432, rs2518884246, rs2518885322, rs2518892925, rs2518884516, rs2518884524, rs879255583, rs879255584, rs1923775114, rs1569233549, rs1569230006, rs1569231897 View all (9 more)	RCV000087143 RCV001788508 RCV001775348 RCV002226896 RCV003333787 RCV003333796 RCV003333797 RCV003333800 RCV003333801 RCV003333742 RCV000721130 RCV000239554 RCV000239467 RCV000239579 RCV000239489 RCV003883297 RCV003883369 RCV004555074 RCV003333750 RCV000995508 RCV001253343 RCV001253788 RCV001263498 RCV001270442
See cases	Pathogenic	rs879255584	RCV002252041

Show/Hide Unknown Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs1602157389	RCV005902064
EBV-positive nodal T- and NK-cell lymphoma	Likely benign	rs2518888022	RCV004560192
Familial cancer of breast	Benign; Likely benign	rs192492405	RCV005899558
Gastric cancer	Benign; Likely benign	rs143534990	RCV005899560
Global developmental delay	Uncertain significance	rs953773970	RCV001553541
Intellectual disability, X-linked 81	Uncertain significance	rs764804263	RCV005248570
Melanoma	Benign; Likely benign	rs192492405	RCV005899559
Microcephaly	Benign; Likely benign	rs193252755	RCV001252697
Neurodevelopmental disorder	Uncertain significance	rs771033388, rs2147182703	RCV001375005 RCV001780063
Non-syndromic X-linked intellectual disability	Uncertain significance	rs1924837336	RCV005359849
Nonpapillary renal cell carcinoma	Likely benign; Uncertain significance	rs374361593, rs913431577, rs201381518	RCV005921097 RCV005931989 RCV005913537
Rare genetic intellectual disability	Uncertain significance	rs371136650	RCV001257020
Thyroid cancer, nonmedullary, 1	Likely benign; Uncertain significance; Benign; Conflicting classifications of pathogenicity	rs775225884, rs1394179466, rs2147179586, rs139133236, rs374361593, rs2147182640, rs2518893168, rs2518885538, rs2518873619, rs2518879737, rs1064796023, rs748967139, rs138602675, rs149158671, rs150746088, rs201381518, rs761467131 View all (2 more)	RCV005912768 RCV005912785 RCV005917572 RCV005925767 RCV005921098 RCV005930047 RCV005930090 RCV005926537 RCV005927084 RCV005931324 RCV005901207 RCV005901412 RCV005906987 RCV005907004 RCV005903197 RCV005913538 RCV005909116

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
ATR X syndrome	Associate	34479510
Brain Diseases	Associate	29314583
Chronic Traumatic Encephalopathy	Associate	29338612
Endometrial Neoplasms	Associate	37671947
Epilepsies Myoclonic	Associate	29314583
Epilepsy	Associate	28972156
Epilepsy Absence	Associate	36842888
Epilepsy Idiopathic Generalized	Associate	36842888
Epileptic Encephalopathy Early Infantile 3	Associate	37271660
Intellectual Disability	Associate	28972156, 34479510
Myoclonic Epilepsy Juvenile	Associate	36842888
Neoplasms	Associate	37671947
Seizures	Associate	29314583

CLCN4 (chloride voltage-gated channel 4)