CACNA1F (calcium voltage-gated channel subunit alpha1 F)

Gene

• Entrez ID: 778
• Gene name: Calcium voltage-gated channel subunit alpha1 F
• Gene symbol: CACNA1F
• Synonyms: AIED, COD3, COD4, CORDX, CORDX3, CSNB2, CSNB2A, CSNBX2, Cav1.4, Cav1.4alpha1, JM8, JMC8, OA2
• Chromosome: X
• Chromosome location: Xp11.23
• Summary: This gene encodes a multipass transmembrane protein that functions as an alpha-1 subunit of the voltage-dependent calcium channel, which mediates the influx of calcium ions into the cell. The encoded protein forms a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Mutations in this gene can cause X-linked eye disorders, including congenital stationary night blindness type 2A, cone-rod dystropy, and Aland Island eye disease. Alternatively spliced transcript variants encoding multiple isoforms have been observed. [provided by RefSeq, Aug 2013]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs80359870	->G	Pathogenic	Coding sequence variant, frameshift variant
rs122456133	C>T	Pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs122456134	G>A	Pathogenic	Coding sequence variant, stop gained
rs122456135	G>A	Pathogenic	Coding sequence variant, stop gained, 5 prime UTR variant
rs122456136	A>G	Pathogenic	Coding sequence variant, missense variant, genic upstream transcript variant
rs138447882	C>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant
rs141010716	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant, genic upstream transcript variant
rs144131971	G>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs149685267	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs781923856	C>T	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs782362725	G>A,T	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs782575860	C>T	Pathogenic	Intron variant, genic upstream transcript variant, splice donor variant
rs782581701	G>A	Pathogenic	Stop gained, coding sequence variant
rs782740998	G>A	Pathogenic	Stop gained, coding sequence variant
rs797044676	G>A	Pathogenic	Intron variant, stop gained, coding sequence variant, genic upstream transcript variant
rs863223294	GACGC>CCA	Pathogenic	Splice acceptor variant, coding sequence variant
rs863225090	C>T	Pathogenic	Missense variant, upstream transcript variant, coding sequence variant, genic upstream transcript variant
rs879255389	C>A,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs886039559	G>A	Likely-pathogenic, pathogenic	Stop gained, coding sequence variant, genic upstream transcript variant
rs886039560	G>A	Pathogenic	Intron variant, stop gained, coding sequence variant, genic upstream transcript variant
rs886041479	C>-	Pathogenic	Splice acceptor variant, coding sequence variant, genic upstream transcript variant
rs886044841	C>T	Pathogenic	Upstream transcript variant, splice donor variant, genic upstream transcript variant
rs1057516199	T>C	Likely-pathogenic	Splice acceptor variant
rs1057518829	T>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, stop gained
rs1057523895	T>G	Likely-pathogenic	Splice acceptor variant
rs1064794711	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1064797371	C>T	Likely-pathogenic	Splice donor variant
rs1085307529	G>A,C,T	Likely-pathogenic	Genic upstream transcript variant, upstream transcript variant, intron variant
rs1358925739	T>C	Likely-pathogenic	Genic upstream transcript variant, splice acceptor variant
rs1365490247	G>A,C	Pathogenic	Stop gained, coding sequence variant, missense variant, genic upstream transcript variant
rs1557105474	CA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1557106008	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1557106557	G>A	Pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs1557107192	TG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1557107417	A>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1557108147	C>T	Likely-pathogenic	Splice donor variant
rs1557109796	TCGGC>-	Likely-pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant
rs1557109912	CTCACAGGCAGCGTGTACAGCTGGCCAGAGCCCCCTCC>-	Likely-pathogenic	Intron variant, genic upstream transcript variant, coding sequence variant, splice donor variant
rs1557110046	->A	Likely-pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant
rs1557110192	G>-	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant
rs1557110499	AAG>-	Pathogenic, likely-pathogenic	Genic upstream transcript variant, inframe deletion, coding sequence variant
rs1557110988	G>A	Likely-pathogenic	Genic upstream transcript variant, stop gained, coding sequence variant
rs1602627593	C>T	Likely-pathogenic	Coding sequence variant, missense variant
rs1602628429	C>T	Likely-pathogenic	Intron variant
rs1602630650	C>T	Pathogenic	Coding sequence variant, stop gained
rs1602639528	AT>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1602639607	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1602641426	C>A	Pathogenic	Coding sequence variant, genic upstream transcript variant, upstream transcript variant, stop gained
rs1602644716	A>C	Pathogenic	Coding sequence variant, genic upstream transcript variant, missense variant
rs1602653110	T>C	Pathogenic	Genic upstream transcript variant, splice acceptor variant
rs1602653742	C>T	Likely-pathogenic	Genic upstream transcript variant, splice acceptor variant
rs1602658505	->GCCACTG	Pathogenic	Coding sequence variant, genic upstream transcript variant, frameshift variant, intron variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0005245	Function	Voltage-gated calcium channel activity	IBA	21873635
GO:0005245	Function	Voltage-gated calcium channel activity	IDA	15897456, 27226626
GO:0005886	Component	Plasma membrane	TAS
GO:0005891	Component	Voltage-gated calcium channel complex	IDA	15897456
GO:0006816	Process	Calcium ion transport	IBA	21873635
GO:0007601	Process	Visual perception	IMP	9662399, 9662400, 16505158
GO:0008331	Function	High voltage-gated calcium channel activity	IBA	21873635
GO:0016021	Component	Integral component of membrane	IDA	15897456
GO:0034765	Process	Regulation of ion transmembrane transport	IEA
GO:0043204	Component	Perikaryon	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050908	Process	Detection of light stimulus involved in visual perception	IMP
GO:0061337	Process	Cardiac conduction	TAS
GO:0070509	Process	Calcium ion import	IBA	21873635
GO:0070588	Process	Calcium ion transmembrane transport	IEA

Other IDs

• MIM: 300110
• HGNC: 1393
• e!Ensembl: ENSG00000102001

Protein

• UniProt ID: O60840
• Protein name: Voltage-dependent L-type calcium channel subunit alpha-1F (Voltage-gated calcium channel subunit alpha Cav1.4)
• Protein function: [Isoform 1]: Voltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. The isoform alpha-1F gives rise to L-type calcium currents. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group. They are blocked by dihydropyridines (DHP), phenylalkylamines, and by benzothiazepines. Activates at more negative voltages and does not undergo calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarization. ; [Isoform 4]: Voltage-dependent L-type calcium channel activates at more hyperpolarized voltages and exhibits a robust calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarizations. ; [Isoform 6]: Voltage-dependent L-type calcium channel activates at more hyperpolarized voltages and exibits a robust calcium-dependent inactivation (CDI), due to incoming calcium ions, during depolarizations.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00520	Ion_trans	91 → 383	Ion transport protein	Family
  PF00520	Ion_trans	528 → 768	Ion transport protein	Family
  PF00520	Ion_trans	870 → 1148	Ion transport protein	Family
  PF00520	Ion_trans	1189 → 1452	Ion transport protein	Family
  PF16905	GPHH	1461 → 1514	Voltage-dependent L-type calcium channel, IQ-associated	Family
  PF08763	Ca_chan_IQ	1524 → 1598	Voltage gated calcium channel IQ domain	Domain
  PF16885	CAC1F_C	1619 → 1976	Voltage-gated calcium channel subunit alpha, C-term	Family

• Sequence:

  MSESEGGKDTTPEPSPANGAGPGPEWGLCPGPPAVEGESSGASGLGTPKRRNQHSKHKTV
  AVASAQRSPRALFCLTLANPLRRSCISIVEWKPFDILILLTIFANCVALGVYIPFPEDDS
  NTANHNLEQVEYVFLVIFTVETVLKIVAYGLVLHPSAYIRNGWNLLDFIIVVVGLFSVLL
  EQGPGRPGDAPHTGGKPGGFDVKALRAFRVLRPLRLVSGVPSLHIVLNSIMKALVPLLHI
  ALLVLFVIIIYAIIGLELFLGRMHKTCYFLGSDMEAEEDPSPCASSGSGRACTLNQTECR
  GRWPGPNGGITNFDNFFFAMLTVFQCVTMEGWTDVLYWMQDAMGYELPWVYFVSLVIFGS
  FFVLNLVLGVLSGEFSKEREKAKARGDFQKQREKQQMEEDLRGYLDWITQAEELDMEDPS
  ADDNLGSMAEEGRAGHRPQLAELTNRRRGRLRWFSHSTRSTHSTSSHASLPASDTGSMTE
  TQGDEDEEEGALASCTRCLNKIMKTRVCRRLRRANRVLRARCRRAVKSNACYWAVLLLVF
  LNTLTIASEHHGQPVWLTQIQEYANKVLLCLFTVEMLLKLYGLGPSAYVSSFFNRFDCFV
  VCGGILETTLVEVGAMQPLGISVLRCVRLLRIFKVTRHWASLSNLVASLLNSMKSIASLL
  LLLFLFIIIFSLLGMQLFGGKFNFDQTHTKRSTFDTFPQALLTVFQILTGEDWNVVMYDG
  IMAYGGPFFPGMLVCIYFIILFICGNYILLNVFLAIAVDNLASGDAGTAKDKGGEKSNEK
  DLPQENEGLVPGVEKEEEEGARREGADMEEEEEEEEEEEEEEEEEGAGGVELLQEVVPKE
  KVVPIPEGSAFFCLSQTNPLRKGCHTLIHHHVFTNLILVFIILSSVSLAAEDPIRAHSFR
  NHILGYFDYAFTSIFTVEILLKMTVFGAFLHRGSFCRSWFNMLDLLVVSVSLISFGIHSS
  AISVVKILRVLRVLRPLRAINRAKGLKHVVQCVFVAIRTIGNIMIVTTLLQFMFACIGVQ
  LFKGKFYTCTDEAKHTPQECKGSFLVYPDGDVSRPLVRERLWVNSDFNFDNVLSAMMALF
  TVSTFEGWPALLYKAIDAYAEDHGPIYNYRVEISVFFIVYIIIIAFFMMNIFVGFVIITF
  RAQGEQEYQNCELDKNQRQCVEYALKAQPLRRYIPKNPHQYRVWATVNSAAFEYLMFLLI
  LLNTVALAMQHYEQTAPFNYAMDILNMVFTGLFTIEMVLKIIAFKPKHYFTDAWNTFDAL
  IVVGSIVDIAVTEVNNGGHLGESSEDSSRISITFFRLFRVMRLVKLLSKGEGIRTLLWTF
  IKSFQALPYVALLIAMIFFIYAVIGMQMFGKVALQDGTQINRNNNFQTFPQAVLLLFRCA
  TGEAWQEIMLASLPGNRCDPESDFGPGEEFTCGSNFAIAYFISFFMLCAFLIINLFVAVI
  MDNFDYLTRDWSILGPHHLDEFKRIWSEYDPGAKGRIKHLDVVALLRRIQPPLGFGKLCP
  HRVACKRLVAMNMPLNSDGTVTFNATLFALVRTSLKIKTEGNLEQANQELRIVIKKIWKR
  MKQKLLDEVIPPPDEEEVTVGKFYATFLIQDYFRKFRRRKEKGLLGNDAAPSTSSALQAG
  LRSLQDLGPEMRQALTCDTEEEEEEGQEGVEEEDEKDLETNKATMVSQPSARRGSGISVS
  LPVGDRLPDSLSFGPSDDDRGTPTSSQPSVPQAGSNTHRRGSGALIFTIPEEGNSQPKGT
  KGQNKQDEDEEVPDRLSYLDEQAGTPPCSVLLPPHRAQRYMDGHLVPRRRLLPPTPAGRK
  PSFTIQCLQRQGSCEDLPIPGTYHRGRNSGPNRAQGSWATPPQRGRLLYAPLLLVEEGAA
  GEGYLGRSSGPLRTFTCLHVPGTHSDPSHGKRGSADSLVEAVLISEGLGLFARDPRFVAL
  AKQEIADACRLTLDEMDNAASDLLAQGTSSLYSDEESILSRFDEEDLGDEMACVHAL

• Sequence length: 1977