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

Gene Gene SNPs Other IDs Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	779
Gene name Gene Name - the full gene name approved by the HGNC.	Calcium voltage-gated channel subunit alpha1 S
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	CACNA1S
Synonyms (NCBI Gene) Gene synonyms aliases	CACNL1A3, CCHL1A3, CMYO18, CMYP18, Cav1.1, DHPRM, HOKPP, HOKPP1, MHS5, TTPP1, hypoPP
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1q32.1
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes one of the five subunits of the slowly inactivating L-type voltage-dependent calcium channel in skeletal muscle cells. Mutations in this gene have been associated with hypokalemic periodic paralysis, thyrotoxic periodic paralysis and mal

Show/Hide all(41)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1325310	C>G,T	Benign, risk-factor	Intron variant
rs1800559	C>A,T	Drug-response, risk-factor	Coding sequence variant, missense variant
rs2281845	C>A,G,T	Benign, risk-factor	Upstream transcript variant
rs2297902	G>A,C	Benign, pathogenic	Missense variant, coding sequence variant, synonymous variant
rs28930068	C>T	Pathogenic	Coding sequence variant, missense variant
rs28930069	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs28986463	T>C	Risk-factor	Intron variant
rs80338777	C>A,T	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs80338778	G>A,C	Pathogenic	Missense variant, coding sequence variant
rs80338779	C>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant
rs116347156	C>G,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs139956524	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Missense variant, coding sequence variant
rs141204958	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, stop gained, missense variant
rs145910245	T>A,G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, missense variant
rs146696298	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs148317787	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs201998231	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs267606698	A>T	Pathogenic	Missense variant, coding sequence variant
rs530655602	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs563795648	G>A,T	Pathogenic	Coding sequence variant, missense variant, stop gained
rs762294904	G>A,T	Pathogenic	Stop gained, synonymous variant, coding sequence variant
rs763794604	C>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs764710968	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs771706267	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs772226819	G>A	Uncertain-significance, drug-response	Missense variant, coding sequence variant
rs797045031	T>C	Pathogenic	Splice acceptor variant
rs1553248947	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1553252746	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1558056376	C>G,T	Likely-pathogenic, uncertain-significance	Splice donor variant
rs1558071742	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1558075630	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1558079311	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1572023336	A>G	Likely-pathogenic	Splice donor variant
rs1572033599	C>T	Likely-pathogenic	Splice donor variant
rs1572035834	C>T	Pathogenic	Coding sequence variant, stop gained
rs1572036396	T>G	Likely-pathogenic	Splice acceptor variant
rs1572038993	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1572039465	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1572048220	C>T	Pathogenic	Coding sequence variant, stop gained
rs1572049461	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1572059904	G>C	Pathogenic	Coding sequence variant, stop gained

Show/Hide all(8)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029696	hsa-miR-26b-5p	Microarray	19088304
MIRT2192292	hsa-miR-4650-5p	CLIP-seq
MIRT2385456	hsa-miR-1321	CLIP-seq
MIRT2385457	hsa-miR-4419a	CLIP-seq
MIRT2385458	hsa-miR-4510	CLIP-seq
MIRT2385459	hsa-miR-4728-5p	CLIP-seq
MIRT2385460	hsa-miR-4739	CLIP-seq
MIRT2385461	hsa-miR-4756-5p	CLIP-seq

Show/Hide all(53)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001501	Process	Skeletal system development	IEA
GO:0002074	Process	Extraocular skeletal muscle development	IEA
GO:0005216	Function	Monoatomic ion channel activity	IEA
GO:0005245	Function	Voltage-gated calcium channel activity	IDA	9852570
GO:0005245	Function	Voltage-gated calcium channel activity	IEA
GO:0005245	Function	Voltage-gated calcium channel activity	IMP	28012042
GO:0005262	Function	Calcium channel activity	IEA
GO:0005515	Function	Protein binding	IPI	12080061, 22153077, 25416956, 32296183
GO:0005516	Function	Calmodulin binding	IEA
GO:0005737	Component	Cytoplasm	IDA	11206130
GO:0005886	Component	Plasma membrane	IDA	11206130
GO:0005886	Component	Plasma membrane	IEA
GO:0005891	Component	Voltage-gated calcium channel complex	IBA
GO:0005891	Component	Voltage-gated calcium channel complex	IDA	9852570
GO:0005891	Component	Voltage-gated calcium channel complex	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006816	Process	Calcium ion transport	IDA	9852570
GO:0006816	Process	Calcium ion transport	IEA
GO:0006816	Process	Calcium ion transport	IEA
GO:0006936	Process	Muscle contraction	IEA
GO:0006936	Process	Muscle contraction	IEA
GO:0006936	Process	Muscle contraction	IMP	17418573, 28012042
GO:0006941	Process	Striated muscle contraction	IEA
GO:0007029	Process	Endoplasmic reticulum organization	IEA
GO:0007519	Process	Skeletal muscle tissue development	IEA
GO:0007520	Process	Myoblast fusion	IEA
GO:0007528	Process	Neuromuscular junction development	IEA
GO:0008331	Function	High voltage-gated calcium channel activity	IBA
GO:0008331	Function	High voltage-gated calcium channel activity	IDA	9852570
GO:0016020	Component	Membrane	IEA
GO:0016529	Component	Sarcoplasmic reticulum	IEA
GO:0030315	Component	T-tubule	IDA	17204937
GO:0030315	Component	T-tubule	IEA
GO:0030315	Component	T-tubule	IMP	28012042
GO:0030315	Component	T-tubule	NAS	27273705
GO:0031674	Component	I band	IDA	11206130
GO:0034220	Process	Monoatomic ion transmembrane transport	IEA
GO:0034702	Component	Monoatomic ion channel complex	IEA
GO:0036094	Function	Small molecule binding	EXP	18761102, 21525002
GO:0043501	Process	Skeletal muscle adaptation	IEA
GO:0045933	Process	Positive regulation of muscle contraction	NAS	22982493
GO:0046872	Function	Metal ion binding	IEA
GO:0048741	Process	Skeletal muscle fiber development	IEA
GO:0051209	Process	Release of sequestered calcium ion into cytosol	IMP	28012042
GO:0055001	Process	Muscle cell development	IEA
GO:0055085	Process	Transmembrane transport	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0070588	Process	Calcium ion transmembrane transport	NAS	22982493
GO:0071313	Process	Cellular response to caffeine	ISS
GO:0098703	Process	Calcium ion import across plasma membrane	IBA
GO:0140677	Function	Molecular function activator activity	EXP	18761102, 21525002
GO:1990454	Component	L-type voltage-gated calcium channel complex	ISO
GO:1990454	Component	L-type voltage-gated calcium channel complex	ISS

MIM	HGNC	e!Ensembl
114208	1397	ENSG00000081248

Protein

UniProt ID

Q13698

Protein name

Voltage-dependent L-type calcium channel subunit alpha-1S (Calcium channel, L type, alpha-1 polypeptide, isoform 3, skeletal muscle) (Voltage-gated calcium channel subunit alpha Cav1.1)

Protein function

Pore-forming, alpha-1S subunit of the voltage-gated calcium channel that gives rise to L-type calcium currents in skeletal muscle. Calcium channels containing the alpha-1S subunit play an important role in excitation-contraction coupling in skel

PDB

2VAY , 6B27

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00520	Ion_trans	50 → 345	Ion transport protein	Family
PF00520	Ion_trans	431 → 672	Ion transport protein	Family
PF00520	Ion_trans	798 → 1076	Ion transport protein	Family
PF00520	Ion_trans	1117 → 1392	Ion transport protein	Family
PF16905	GPHH	1401 → 1454	Voltage-dependent L-type calcium channel, IQ-associated	Family
PF08763	Ca_chan_IQ	1464 → 1538	Voltage gated calcium channel IQ domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Skeletal muscle specific.

Sequence

MEPSSPQDEGLRKKQPKKPVPEILPRPPRALFCLTLENPLRKACISIVEWKPFETIILLT
IFANCVALAVYLPMPEDDNNSLNLGLEKLEYFFLIVFSIEAAMKIIAYGFLFHQDAYLRS
GWNVLDFTIVFLGVFTVILEQVNVIQSHTAPMSSKGAGLDVKALRAFRVLRPLRLVSGVP
SLQVVLNSIFKAMLPLFHIALLVLFMVIIYAIIGLELFKGKMHKTCYFIGTDIVATVENE
EPSPCARTGSGRRCTINGSECRGGWPGPNHGITHFDNFGFSMLTVYQCITMEGWTDVLYW
VNDAIGNEWPWIYFVTLILLGSFFILNLVLGVLSGEFTKEREKAKSRGTFQKLREKQQLD
EDLRGYMSWITQGEVMDVEDFREGKLSLDEGGSDTESLYEIAGLNKIIQFIRHWRQWNRI
FRWKCHDIVKSKVFYWLVILIVALNTLSIASEHHNQPLWLTRLQDIANRVLLSLFTTEML
MKMYGLGLRQYFMSIFNRFDCFVVCSGILEILLVESGAMTPLGISVLRCIRLLRIFKITK
YWTSLSNLVASLLNSIRSIASLLLLLFLFIVIFALLGMQLFGGRYDFEDTEVRRSNFDNF
PQALISVFQVLTGEDWTSMMYNGIMAYGGPSYPGMLVCIYFIILFVCGNYILLNVFLAIA
VDNLAEAESLTSAQKAKAEEKKRRKMSKGLPDKSEEEKSTMAKKLEQKPKGEGIPTTAKL
KIDEFESNVNEVKDPYPSADFPGDDEEDEPEIPLSPRPRPLAELQLKEKAVPIPEASSFF
IFSPTNKIRVLCHRIVNATWFTNFILLFILLSSAALAAEDPIRADSMRNQILKHFDIGFT
SVFTVEIVLKMTTYGAFLHKGSFCRNYFNMLDLLVVAVSLISMGLESSAISVVKILRVLR
VLRPLRAINRAKGLKHVVQCMFVAISTIGNIVLVTTLLQFMFACIGVQLFKGKFFRCTDL
SKMTEEECRGYYYVYKDGDPMQIELRHREWVHSDFHFDNVLSAMMSLFTVSTFEGWPQLL
YKAIDSNAEDVGPIYNNRVEMAIFFIIYIILIAFFMMNIFVGFVIVTFQEQGETEYKNCE
LDKNQRQCVQYALKARPLRCYIPKNPYQYQVWYIVTSSYFEYLMFALIMLNTICLGMQHY
NQSEQMNHISDILNVAFTIIFTLEMILKLMAFKARGYFGDPWNVFDFLIVIGSIIDVILS
EIDTFLASSGGLYCLGGGCGNVDPDESARISSAFFRLFRVMRLIKLLSRAEGVRTLLWTF
IKSFQALPYVALLIVMLFFIYAVIGMQMFGKIALVDGTQINRNNNFQTFPQAVLLLFRCA
TGEAWQEILLACSYGKLCDPESDYAPGEEYTCGTNFAYYYFISFYMLCAFLVINLFVAVI
MDNFDYLTRDWSILGPHHLDEFKAIWAEYDPEAKGRIKHLDVVTLLRRIQPPLGFGKFCP
HRVACKRLVGMNMPLNSDGTVTFNATLFALVRTALKIKTEGNFEQANEELRAIIKKIWKR
TSMKLLDQVIPPIGDDEVTVGKFYATFLIQEHFRKFMKRQEEYYGYRPKKDIVQIQAGLR
TIEEEAAPEICRTVSGDLAAEEELERAMVEAAMEEGIFRRTGGLFGQVDNFLERTNSLPP
VMANQRPLQFAEIEMEEMESPVFLEDFPQDPRTNPLARANTNNANANVAYGNSNHSNSHV
FSSVHYEREFPEETETPATRGRALGQPCRVLGPHSKPCVEMLKGLLTQRAMPRGQAPPAP
CQCPRVESSMPEDRKSSTPGSLHEETPHSRSTRENTSRCSAPATALLIQKALVRGGLGTL
AADANFIMATGQALADACQMEPEEVEIMATELLKGREAPEGMASSLGCLNLGSSLGSLDQ
HQGSQETLIPPRL

Sequence length

1873

Interactions

View interactions

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
congenital myopathy	Congenital myopathy 18	rs28930068, rs80338778	N/A
Hypokalemic Periodic Paralysis	Hypokalemic periodic paralysis, type 1, hypokalemic periodic paralysis	rs1287079817, rs28930068, rs1572049461, rs1572023336, rs28930069, rs80338778, rs80338777, rs267606698, rs367983954, rs1558056376, rs148317787	N/A

Show/Hide Unknown Diseases (4)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Biliary Cholangitis	Primary biliary cholangitis	N/A	N/A	GWAS
Hereditary Liability To Pressure Palsies	hereditary liability to pressure palsies	N/A	N/A	ClinVar
Long QT Syndrome	long qt syndrome	N/A	N/A	ClinVar
Thyrotoxic Periodic Paralysis	Thyrotoxic periodic paralysis, susceptibility to, 1	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (54)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adrenal Hyperplasia Congenital	Associate	25430699
Andersen Syndrome	Associate	33345742, 9132138
Anodontia	Associate	38157055
Arrhythmias Cardiac	Associate	9132138
Arthritis Psoriatic	Associate	16622521
Arthritis Rheumatoid	Associate	16622521
Arthrogryposis	Associate	33060286
Autism Spectrum Disorder	Associate	35220405
Central Nervous System Vascular Malformations	Associate	33060286
Channelopathies	Associate	27199537
Clubfoot	Associate	31227654
Cognition Disorders	Associate	31227654
Contracture	Associate	31227654
Depressive Disorder	Associate	35590255
Eccrine Porocarcinoma	Associate	34045664
Fatigue	Associate	37679049
Fatigue Syndrome Chronic	Associate	37679049
Graves Disease	Associate	39333966
Heart Failure	Inhibit	1326001
Heat Stress Disorders	Associate	25658027
Hypertension	Associate	32111194
Hyperthyroidism	Associate	37876543, 39333966
Hypokalemic Periodic Paralysis	Associate	11034874, 15098604, 15716625, 18162704, 19118277, 22901280, 29138267, 30420713, 31380823, 32104981, 33389921, 34120654, 34463712, 37656291, 39333966, 7847370, 9132138, 9307251 View all (3 more)
Hypothermia	Associate	35414440
Kidney Failure Chronic	Associate	1326001
Lagophthalmos	Associate	15716625, 25430699, 33389921
Lipoma	Associate	27199537
Malignant Hyperthermia	Associate	19825159, 25658027, 33564012, 35835312, 36318155, 40262809
Mental Disorders	Associate	35220405
Microcystic adnexal carcinoma	Stimulate	35509066
Muscle Hypotonia	Associate	31227654
Muscle Neoplasms	Associate	37679049
Muscle Weakness	Associate	22901280, 34120654, 37656291, 37679049
Muscular Atrophy	Associate	37679049
Muscular Diseases	Associate	30325262, 35543701, 36318155, 7650604
Muscular Dystrophies Limb Girdle	Associate	29970176
Musculoskeletal Abnormalities	Associate	28779239
Myalgia	Associate	37679049
Myasthenia Gravis Autoimmune Experimental	Associate	24719132
Myocardial Stunning	Associate	1326001
Myostatin related muscle hypertrophy	Associate	37679049
Myotonia Congenita	Associate	29950399, 31227654
Neuromuscular Manifestations	Associate	32104981
Ophthalmoplegia	Associate	31227654
Paralyses Familial Periodic	Associate	25430699, 31068157, 31380823, 33345742, 34120654, 35039355, 37656291, 7650604
Paralysis	Associate	31380823
Paralysis Hyperkalemic Periodic	Associate	33345742
Primary Release Disorder Of Platelets	Associate	36318155
Ptosis Hereditary Congenital 2	Associate	37679049
Pulmonary Atelectasis	Associate	15098604
Respiratory Insufficiency	Associate	31227654
Rhabdomyolysis	Associate	28779239
Schizophrenia	Associate	35220405
Ventricular Dysfunction Left	Associate	1326001

CACNA1S (calcium voltage-gated channel subunit alpha1 S)