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

Summary

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: mouse all
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Genomic context

Location:: Xp11.23

Exon count:: 48

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (49205063..49233340, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (48616922..48645225, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (49061523..49089802, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
Strikingly High Myopia in Aland Island Eye Disease.
Title: Strikingly High Myopia in Aland Island Eye Disease.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

DXS8060 (e-PCR), detects polymorphism
- UniSTS:24132

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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables voltage-gated calcium channel activity	IDA Inferred from Direct Assay 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 detection of light stimulus involved in visual perception	IMP Inferred from Mutant Phenotype more info
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

NG_009095.2 RefSeqGene

Range

5027..33304

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

49205063..49233340 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

48616922..48645225 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327857.1 → XP_054183832.1 voltage-dependent L-type calcium channel subunit alpha-1F isoform X2
XM_054327856.1 → XP_054183831.1 voltage-dependent L-type calcium channel subunit alpha-1F isoform X1