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CABP4 calcium binding protein 4 [ Homo sapiens (human) ]

Gene ID: 57010, updated on 29-Mar-2020

Summary

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Official Symbol
CABP4provided by HGNC
Official Full Name
calcium binding protein 4provided by HGNC
Primary source
HGNC:HGNC:1386
See related
Ensembl:ENSG00000175544 MIM:608965
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
CRSD; CSNB2B
Summary
This gene encodes a member of the CABP family of calcium binding protein characterized by four EF-hand motifs. Mutations in this gene are associated with congenital stationary night blindness type 2B. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
Expression
Biased expression in spleen (RPKM 2.4), prostate (RPKM 0.5) and 12 other tissues See more
Orthologs
mouse all

Genomic context

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See CABP4 in Genome Data Viewer
Location:
11q13.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (67452403..67461774)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67219886..67229245)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein S6 kinase B2 Neighboring gene protein tyrosine phosphatase receptor type C associated protein Neighboring gene coronin 1B Neighboring gene G protein-coupled receptor 152 Neighboring gene transmembrane protein 134 Neighboring gene aryl hydrocarbon receptor interacting protein Neighboring gene microRNA 6752 Neighboring gene phosphatidylinositol transfer protein membrane associated 1

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
  • 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. Retinal findings in a patient of French ancestry with CABP4-related retinal disease. Smirnov VM, et al. Doc Ophthalmol, 2018 Apr. PMID 29525873
  2. Multimodal imaging in CABP4-related retinopathy. Schatz P, et al. Ophthalmic Genet, 2017 Sep-Oct. PMID 28635425
  3. A null mutation in CABP4 causes Leber's congenital amaurosis-like phenotype. Aldahmesh MA, et al. Mol Vis, 2010 Feb 10. PMID 20157620, Free PMC Article
  4. A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder. Littink KW, et al. Invest Ophthalmol Vis Sci, 2009 May. PMID 19074807
  5. Different sorting of Lys-Asp-Glu-Leu proteins in rat liver. Peter F, et al. J Biol Chem, 1992 May 25. PMID 1316906

See all (22) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CABP4-related retinal disease is a cone-rod system disorder with possible foveal abnormalities.
    Title: Retinal findings in a patient of French ancestry with CABP4-related retinal disease.
  2. Foveal thinning is a feature of CABP4 retinopathy. Normal autofluorescence is consistent with inner retinal dysfunction and suggests the condition could be amenable to gene therapy. Retinal dysfunction was stable throughout follow-up.
    Title: Multimodal imaging in CABP4-related retinopathy.
  3. In this study, a novel compound heterozygous mutation, c.[1A>G]; [608G>T] (p.[0?]; p.[W203L]), was identified in the LRIT3 gene of a proband. No mutations were identified in the CABP4 or GPR179 gene.
    Title: Mutation screening of the LRIT3, CABP4, and GPR179 genes in Chinese patients with Schubert-Bornschein congenital stationary night blindness.
  4. Twenty-nine CACNA1F variations were detected among 34 families in the total cohort, and a novel CABP4 variation was identified in one family.
    Title: Clinical Characteristics, Mutation Spectrum, and Prevalence of Åland Eye Disease/Incomplete Congenital Stationary Night Blindness in Denmark.
  5. we found a homozygous compound mutation in the CABP4 gene in 3 patients with congenital stationary night blindess 2.
    Title: Genotype and phenotype of 101 dutch patients with congenital stationary night blindness.
  6. Complex regulation of voltage-dependent activation and inactivation properties of retinal voltage-gated Cav1.4 L-type Ca2+ channels by Ca2+-binding protein 4 (CaBP4).
    Title: Complex regulation of voltage-dependent activation and inactivation properties of retinal voltage-gated Cav1.4 L-type Ca2+ channels by Ca2+-binding protein 4 (CaBP4).
  7. Observational study of genetic testing. (HuGE Navigator)
    Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
  8. This report significantly expands on the phenotype associated with calcium binding protein 4 mutations.
    Title: A null mutation in CABP4 causes Leber's congenital amaurosis-like phenotype.
  9. A novel homozygous nonsense mutation in CABP4 in two siblings resulted in a phenotype with severely reduced cone function and only negligibly reduced rod function on electroretinography and psychophysical testing.
    Title: A novel homozygous nonsense mutation in CABP4 causes congenital cone-rod synaptic disorder.
  10. it is reported for the first time that mutations in CABP4 lead to autosomal recessive congenital stationary night blindness
    Title: Mutations in CABP4, the gene encoding the Ca2+-binding protein 4, cause autosomal recessive night blindness.
Submit: New GeneRIF Correction

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, type 2B
MedGen: C4041558 OMIM: 610427 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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
calcium channel regulator activity IEA
Inferred from Electronic Annotation
more info
  
calcium ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
calcium ion binding TAS
Traceable Author Statement
more info
 PubMed 
ion channel binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
photoreceptor cell morphogenesis IEA
Inferred from Electronic Annotation
more info
  
phototransduction IEA
Inferred from Electronic Annotation
more info
  
retinal bipolar neuron differentiation IEA
Inferred from Electronic Annotation
more info
  
retinal cone cell development IEA
Inferred from Electronic Annotation
more info
  
signal transduction NAS
Non-traceable Author Statement
more info
 PubMed 
visual perception IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
extracellular region NAS
Non-traceable Author Statement
more info
 PubMed 
synapse TAS
Traceable Author Statement
more info
 PubMed 
terminal bouton TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
calcium-binding protein 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_021211.1 RefSeqGene

    Range
    5008..11428
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001300895.3 → NP_001287824.1  calcium-binding protein 4 isoform b

    See identical proteins and their annotated locations for NP_001287824.1

    Status: REVIEWED

    Source sequence(s)
    AP003419
    Consensus CDS
    CCDS73333.1
    UniProtKB/Swiss-Prot
    P57796
    UniProtKB/TrEMBL
    A0A024R5K4
    Conserved Domains (1) summary
    cl25352
    Location:20 → 169
    EFh_PEF; The penta-EF hand (PEF) family

  2. NM_001300896.3 → NP_001287825.1  calcium-binding protein 4 isoform b

    See identical proteins and their annotated locations for NP_001287825.1

    Status: REVIEWED

    Source sequence(s)
    AP003419
    Consensus CDS
    CCDS73333.1
    UniProtKB/Swiss-Prot
    P57796
    UniProtKB/TrEMBL
    A0A024R5K4
    Related
    ENSP00000401555.2, ENST00000438189.6
    Conserved Domains (1) summary
    cl25352
    Location:20 → 169
    EFh_PEF; The penta-EF hand (PEF) family

  3. NM_001379183.1 → NP_001366112.1  calcium-binding protein 4 isoform b

    Status: REVIEWED

    Source sequence(s)
    AP003419

  4. NM_145200.5 → NP_660201.1  calcium-binding protein 4 isoform a

    See identical proteins and their annotated locations for NP_660201.1

    Status: REVIEWED

    Source sequence(s)
    AP003419
    Consensus CDS
    CCDS8166.1
    UniProtKB/Swiss-Prot
    P57796
    Related
    ENSP00000324960.5, ENST00000325656.6
    Conserved Domains (2) summary
    cl25352
    Location:125 → 274
    EFh_PEF; The penta-EF hand (PEF) family
    cl27975
    Location:12 → 101
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)

RNA

  1. NR_166529.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AP003419

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    67452403..67461774
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017018025.1 → XP_016873514.1  calcium-binding protein 4 isoform X5

    UniProtKB/Swiss-Prot
    P57796
    UniProtKB/TrEMBL
    A0A024R5K4
    Conserved Domains (1) summary
    cl25352
    Location:20 → 169
    EFh_PEF; The penta-EF hand (PEF) family

  2. XM_024448616.1 → XP_024304384.1  calcium-binding protein 4 isoform X5

    Conserved Domains (1) summary
    cl25352
    Location:20 → 169
    EFh_PEF; The penta-EF hand (PEF) family

  3. XM_024448615.1 → XP_024304383.1  calcium-binding protein 4 isoform X2

    Conserved Domains (2) summary
    cl25352
    Location:125 → 274
    EFh_PEF; The penta-EF hand (PEF) family
    cl27975
    Location:12 → 101
    EBV-NA3; Epstein-Barr virus nuclear antigen 3 (EBNA-3)

  4. XM_011545181.2 → XP_011543483.1  calcium-binding protein 4 isoform X1

    Conserved Domains (3) summary
    PHA03415
    Location:81 → 190
    PHA03415; putative internal virion protein; Provisional
    PTZ00184
    Location:145 → 294
    PTZ00184; calmodulin; Provisional
    cd00051
    Location:230 → 293
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

  5. XM_011545182.2 → XP_011543484.1  calcium-binding protein 4 isoform X3

    Conserved Domains (3) summary
    cd00051
    Location:182 → 245
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...
    pfam13499
    Location:149 → 207
    EF-hand_7; EF-hand domain pair
    pfam13833
    Location:154 → 202
    EF-hand_8; EF-hand domain pair

  6. XM_005274114.3 → XP_005274171.2  calcium-binding protein 4 isoform X4

    Conserved Domains (2) summary
    PHA03415
    Location:81 → 190
    PHA03415; putative internal virion protein; Provisional
    cd00051
    Location:153 → 193
    EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

  7. XM_011545183.2 → XP_011543485.1  calcium-binding protein 4 isoform X5

    See identical proteins and their annotated locations for XP_011543485.1

    UniProtKB/Swiss-Prot
    P57796
    UniProtKB/TrEMBL
    A0A024R5K4
    Conserved Domains (1) summary
    cl25352
    Location:20 → 169
    EFh_PEF; The penta-EF hand (PEF) family
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P57796.2 GenPept UniProtKB/Swiss-Prot:P57796

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