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CACNA1F calcium voltage-gated channel subunit alpha1 F [ Homo sapiens (human) ]

Gene ID: 778, updated on 3-Nov-2024

Summary

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Official Symbol
CACNA1Fprovided by HGNC
Official Full Name
calcium voltage-gated channel subunit alpha1 Fprovided by HGNC
Primary source
HGNC:HGNC:1393
See related
Ensembl:ENSG00000102001 MIM:300110; AllianceGenome:HGNC:1393
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
JM8; OA2; AIED; COD3; COD4; JMC8; CORDX; CSNB2; CORDX3; CSNB2A; CSNBX2; Cav1.4; Cav1.4alpha1
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]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See CACNA1F in Genome Data Viewer
Location:
Xp11.23
Exon count:
48
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (49205063..49233340, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (48616922..48645225, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (49061523..49089802, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:49032849-49033350 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 11 Neighboring gene prickle planar cell polarity protein 3 Neighboring gene proteolipid protein 2 Neighboring gene CRISPRi-FlowFISH-validated GATA1 and PLP2 regulatory element Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 12 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29635 Neighboring gene CRISPRi-FlowFISH-validated PLP2 regulatory element 13 Neighboring gene synaptophysin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20842 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20843 Neighboring gene SYP antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:49065732-49066931 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:49086994-49087652 Neighboring gene heat shock protein family B (small) member 1 pseudogene 2 Neighboring gene coiled-coil domain containing 22 Neighboring gene CRISPRi-FlowFISH-validated GATA1 regulatory element 2 Neighboring gene forkhead box P3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The CACNA1F gene encodes an L-type calcium channel with unique biophysical properties and tissue distribution. McRory JE, et al. J Neurosci, 2004 Feb 18. PMID 14973233, Free PMC Article
  2. What can naturally occurring mutations tell us about Ca(v)1.x channel function? Stockner T, et al. Biochim Biophys Acta, 2013 Jul. PMID 23219801, Free PMC Article
  3. Outer retinal structural anomaly due to frameshift mutation in CACNA1F gene. Vincent A, et al. Eye (Lond), 2012 Sep. PMID 22744390, Free PMC Article
  4. A novel p.Gly603Arg mutation in CACNA1F causes Åland island eye disease and incomplete congenital stationary night blindness phenotypes in a family. Vincent A, et al. Mol Vis, 2011. PMID 22194652, Free PMC Article
  5. Alternative splicing at C terminus of Ca(V)1.4 calcium channel modulates calcium-dependent inactivation, activation potential, and current density. Tan GM, et al. J Biol Chem, 2012 Jan 6. PMID 22069316, Free PMC Article

See all (79) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Optic nerve involvement in CACNA1F-related disease: observations from a multicentric case series.
    Title: Optic nerve involvement in CACNA1F-related disease: observations from a multicentric case series.
  2. Assessing the Pathogenicity of In-Frame CACNA1F Indel Variants Using Structural Modeling.
    Title: Assessing the Pathogenicity of In-Frame CACNA1F Indel Variants Using Structural Modeling.
  3. Identification of a novel CACNA1F mutation in a Chinese family with CORDX3.
    Title: Identification of a novel CACNA1F mutation in a Chinese family with CORDX3.
  4. Two novel CACNA1F gene mutations cause two different phenotypes: Aland Eye Disease and incomplete Congenital Stationary Night Blindness.
    Title: Two novel CACNA1F gene mutations cause two different phenotypes: Aland Eye Disease and incomplete Congenital Stationary Night Blindness.
  5. Strikingly High Myopia in Aland Island Eye Disease.
    Title: Strikingly High Myopia in Aland Island Eye Disease.
  6. Optic Atrophy and Inner Retinal Thinning in CACNA1F-related Congenital Stationary Night Blindness.
    Title: Optic Atrophy and Inner Retinal Thinning in CACNA1F-related Congenital Stationary Night Blindness.
  7. A Novel Splice-Site Variant in CACNA1F Causes a Phenotype Synonymous with Aland Island Eye Disease and Incomplete Congenital Stationary Night Blindness.
    Title: A Novel Splice-Site Variant in CACNA1F Causes a Phenotype Synonymous with Åland Island Eye Disease and Incomplete Congenital Stationary Night Blindness.
  8. Functional impact of a congenital stationary night blindness type 2 mutation depends on subunit composition of Cav1.4 Ca(2+) channels.
    Title: Functional impact of a congenital stationary night blindness type 2 mutation depends on subunit composition of Ca(v)1.4 Ca(2+) channels.
  9. An Ashkenazi Jewish founder mutation in CACNA1F gene is associated with congenital stationary night blindness.
    Title: An Ashkenazi Jewish founder mutation in CACNA1F causes retinal phenotype in both hemizygous males and heterozygous female carriers.
  10. Data revealed the presence of intronic and synonymous disease-causing variants leading to miss-splicing of CACNA1F-mediated inherited retinal disorders.
    Title: Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders.
Submit: New GeneRIF Correction See all GeneRIFs (50)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Congenital stationary night blindness 2A
MedGen: C1848172 OMIM: 300071 GeneReviews: X-Linked Congenital Stationary Night Blindness
Compare labs
Ocular albinism, type II
MedGen: C0268505 OMIM: 300600 GeneReviews: Not available
Compare labs
X-linked cone-rod dystrophy 3
MedGen: C1845407 OMIM: 300476 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables high voltage-gated calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables high voltage-gated calcium channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables voltage-gated calcium channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables voltage-gated calcium channel activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in calcium ion import across plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in calcium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in detection of light stimulus involved in visual perception IMP
Inferred from Mutant Phenotype
more info
  
involved_in negative regulation of voltage-gated calcium channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in visual perception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
  
located_in photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
  
part_of voltage-gated calcium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of voltage-gated calcium channel complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
voltage-dependent L-type calcium channel subunit alpha-1F
Names
calcium channel, voltage-dependent, L type, alpha 1F subunit
voltage-gated calcium channel subunit alpha Cav1.4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009095.2 RefSeqGene

    Range
    5027..33304
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256789.3 → NP_001243718.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform 2

    See identical proteins and their annotated locations for NP_001243718.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC232271, AF201304, AJ224874
    Consensus CDS
    CCDS59167.1
    UniProtKB/Swiss-Prot
    O60840
    Related
    ENSP00000321618.6, ENST00000323022.10
    Conserved Domains (4) summary
    pfam00520
    Location:1196 → 1441
    Ion_trans; Ion transport protein
    pfam08763
    Location:1514 → 1585
    Ca_chan_IQ; Voltage gated calcium channel IQ domain
    pfam16885
    Location:1609 → 1963
    CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term
    pfam16905
    Location:1449 → 1512
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  2. NM_001256790.3 → NP_001243719.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform 3

    See identical proteins and their annotated locations for NP_001243719.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate splice sites in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC232271, AF067227, AF201304
    Consensus CDS
    CCDS59166.1
    UniProtKB/Swiss-Prot
    O60840
    Related
    ENSP00000365427.1, ENST00000376251.5
    Conserved Domains (4) summary
    pfam00520
    Location:1142 → 1387
    Ion_trans; Ion transport protein
    pfam08763
    Location:1460 → 1531
    Ca_chan_IQ; Voltage gated calcium channel IQ domain
    pfam16885
    Location:1555 → 1909
    CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term
    pfam16905
    Location:1395 → 1458
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  3. NM_005183.4 → NP_005174.2  voltage-dependent L-type calcium channel subunit alpha-1F isoform 1

    See identical proteins and their annotated locations for NP_005174.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC232271, AF201304
    Consensus CDS
    CCDS35253.1
    UniProtKB/Swiss-Prot
    A6NI29, F5CIQ9, O43901, O60840, O95226, Q9UHB1
    Related
    ENSP00000365441.2, ENST00000376265.2
    Conserved Domains (4) summary
    pfam00520
    Location:1207 → 1452
    Ion_trans; Ion transport protein
    pfam08763
    Location:1525 → 1596
    Ca_chan_IQ; Voltage gated calcium channel IQ domain
    pfam16885
    Location:1620 → 1974
    CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term
    pfam16905
    Location:1460 → 1523
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    49205063..49233340 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543983.3 → XP_011542285.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform X2

    Conserved Domains (4) summary
    pfam00520
    Location:1142 → 1380
    Ion_trans; Ion transport protein
    pfam08763
    Location:1453 → 1524
    Ca_chan_IQ; Voltage gated calcium channel IQ domain
    pfam16885
    Location:1548 → 1902
    CAC1F_C; Voltage-gated calcium channel subunit alpha, C-term
    pfam16905
    Location:1388 → 1451
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

  2. XM_017029836.1 → XP_016885325.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    48616922..48645225 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054327857.1 → XP_054183832.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform X2

  2. XM_054327856.1 → XP_054183831.1  voltage-dependent L-type calcium channel subunit alpha-1F isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60840.2 GenPept UniProtKB/Swiss-Prot:O60840

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