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

Summary

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; AllianceGenome:HGNC:1386
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: all
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Genomic context

Location:: 11q13.2

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (67452403..67461752)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (67446523..67455877)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (67219874..67229223)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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).
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.
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.
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.
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.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Cone-rod synaptic disorder, congenital nonprogressive MedGen: C4041558 OMIM: 610427 GeneReviews: Not available	not available

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

D11S2072 (e-PCR)
- UniSTS:150030

GDB:434012 (e-PCR)
- UniSTS:157204

PMC156606P2 (e-PCR)
- UniSTS:271409

D8S2279 (e-PCR)
- UniSTS:473907

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium channel regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	NAS Non-traceable Author Statement more info	PubMed
enables calcium ion binding	TAS Traceable Author Statement more info	PubMed
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in photoreceptor cell morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in phototransduction	IEA Inferred from Electronic Annotation more info
involved_in retinal bipolar neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in retinal cone cell development	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed
involved_in visual perception	IBA Inferred from Biological aspect of Ancestor more info
involved_in visual perception	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	NAS Non-traceable Author Statement more info	PubMed
located_in synapse	TAS Traceable Author Statement more info	PubMed
located_in 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

NG_021211.1 RefSeqGene

Range

5008..11406

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

PTZ00184
Location:20 → 169

PTZ00184; calmodulin; Provisional
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

Related

ENSP00000401555.2, ENST00000438189.6

Conserved Domains (1) summary

PTZ00184
Location:20 → 169

PTZ00184; calmodulin; Provisional
NM_001379183.1 → NP_001366112.1 calcium-binding protein 4 isoform b

Status: REVIEWED

Source sequence(s)

AP003419

Consensus CDS

CCDS73333.1

Conserved Domains (1) summary

PTZ00184
Location:20 → 169

PTZ00184; calmodulin; Provisional
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, Q8N4Z2, Q8WWY5

Related

ENSP00000324960.5, ENST00000325656.7

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

NR_166529.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AP003419

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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

67452403..67461752

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_024448615.2 → XP_024304383.1 calcium-binding protein 4 isoform X1

UniProtKB/Swiss-Prot

P57796, Q8N4Z2, Q8WWY5

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)
XM_005274114.4 → XP_005274171.2 calcium-binding protein 4 isoform X2

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 ...