CACNA1S (calcium voltage-gated channel subunit alpha1 S)

Gene

• Entrez ID: 779
• Gene name: Calcium voltage-gated channel subunit alpha1 S
• Gene symbol: CACNA1S
• Synonyms: CACNL1A3, CCHL1A3, Cav1.1, HOKPP, HOKPP1, MHS5, TTPP1, hypoPP
• Chromosome: 1
• Chromosome location: 1q32.1
• Summary: 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 malignant hyperthermia susceptibility. [provided by RefSeq, Jul 2008]

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029696	hsa-miR-26b-5p	Microarray	19088304

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005245	Function	Voltage-gated calcium channel activity	IBA	21873635
GO:0005245	Function	Voltage-gated calcium channel activity	IDA	9852570
GO:0005515	Function	Protein binding	IPI	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	TAS
GO:0005891	Component	Voltage-gated calcium channel complex	IDA	9852570
GO:0006816	Process	Calcium ion transport	IBA	21873635
GO:0006816	Process	Calcium ion transport	IDA	9852570
GO:0006936	Process	Muscle contraction	IMP	17418573
GO:0008331	Function	High voltage-gated calcium channel activity	IBA	21873635
GO:0008331	Function	High voltage-gated calcium channel activity	IDA	9852570
GO:0030315	Component	T-tubule	IDA	17204937
GO:0031674	Component	I band	IDA	11206130
GO:0034765	Process	Regulation of ion transmembrane transport	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0061337	Process	Cardiac conduction	TAS
GO:0070509	Process	Calcium ion import	IBA	21873635
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0071313	Process	Cellular response to caffeine	ISS
GO:1990454	Component	L-type voltage-gated calcium channel complex	ISS

Other IDs

• MIM: 114208
• HGNC: 1397
• e!Ensembl: 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 skeletal muscle via their interaction with RYR1, which triggers Ca(2+) release from the sarcplasmic reticulum and ultimately results in muscle contraction. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group.
• 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

• 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