CIB2 calcium and integrin binding family member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CIB2provided by HGNC
Official Full Name: calcium and integrin binding family member 2provided by HGNC
Primary source: HGNC:HGNC:24579
See related: Ensembl:ENSG00000136425 MIM:605564; AllianceGenome:HGNC:24579
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: KIP2; USH1J; DFNB48
Summary: The protein encoded by this gene is similar to that of KIP/CIB, calcineurin B, and calmodulin. The encoded protein is a calcium-binding regulatory protein that interacts with DNA-dependent protein kinase catalytic subunits (DNA-PKcs), and it is involved in photoreceptor cell maintenance. Mutations in this gene cause deafness, autosomal recessive, 48 (DFNB48), and also Usher syndrome 1J (USH1J). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression: Broad expression in small intestine (RPKM 6.5), testis (RPKM 5.9) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q25.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (78104606..78131535, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (75967162..75994101, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (78396948..78423877, complement)

Chromosome 15 - NC_000015.10 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
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?

Calcium- and Integrin-Binding Protein 2 (CIB2) in Physiology and Disease: Bright and Dark Sides.
Title: Calcium- and Integrin-Binding Protein 2 (CIB2) in Physiology and Disease: Bright and Dark Sides.
CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells.
Title: CIB2 and CIB3 are auxiliary subunits of the mechanotransduction channel of hair cells.
Oligomeric state, hydrodynamic properties and target recognition of human Calcium and Integrin Binding protein 2 (CIB2).
Title: Oligomeric state, hydrodynamic properties and target recognition of human Calcium and Integrin Binding protein 2 (CIB2).
This report is the first to show that biallelic LOF variants in CIB2 cause ARNSHL and not USH. In the era of precision medicine, providing the correct diagnosis (NSHL vs USH) is essential for patient care as it impacts potential intervention and prevention options for patients
Title: Variants in CIB2 cause DFNB48 and not USH1J.
this study identifies CIB1 and CIB2 as host helper factors for HIV-1 replication that are required for optimal receptor-mediated viral entry
Title: CIB1 and CIB2 are HIV-1 helper factors involved in viral entry.
results suggest that GJB2 and CIB2 are common cause of hearing loss in different Pakistani ethnicities
Title: Genetic Testing of Non-familial Deaf Patients for CIB2 and GJB2 Mutations: Phenotype and Genetic Counselling.
High CIB2 expression is associated with ovarian Cancer.
Title: CIB2 Negatively Regulates Oncogenic Signaling in Ovarian Cancer via Sphingosine Kinase 1.
Novel homozygous missense variant c.196C>T and compound heterozygous variants, c.[97C>T];[196C>T], were associated with nonsyndromic deafness.
Title: Novel and recurrent CIB2 variants, associated with nonsyndromic deafness, do not affect calcium buffering and localization in hair cells.
We identified a novel variant (rs7164338) on chromosome 15q25.1 in the CIB2 associated with lower pulse wave velocity.
Title: Integrated multiomics approach identifies calcium and integrin-binding protein-2 as a novel gene for pulse wave velocity.
CIB2 (Calcium and Integrin Binding Protein 2) Mutation Associated with Non-Syndromic Hearing Loss in a Hispanic Family
Title: A Novel C-Terminal CIB2 (Calcium and Integrin Binding Protein 2) Mutation Associated with Non-Syndromic Hearing Loss in a Hispanic Family.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Autosomal recessive nonsyndromic hearing loss 48 MedGen: C1836199 OMIM: 609439 GeneReviews: Not available	Compare labs
Usher syndrome type 1J MedGen: C3553944 OMIM: 614869 GeneReviews: Usher Syndrome Type I	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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 replication, specifically viral entry, requires CIB1 and CIB2 expression as shRNA knockdown of each impairs replication in Jurkat and primary CD4+ T cells	PubMed
Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies calcium and integrin binding family member 2 (CIB2) is important for HIV-1 replication	PubMed
Knockdown of calcium and integrin binding family member 2 (CIB2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-D60668 (e-PCR)
- UniSTS:4893

G62031 (e-PCR)
- UniSTS:139120

WI-17359 (e-PCR)
- UniSTS:39304

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables integrin binding	IEA Inferred from Electronic Annotation more info
enables magnesium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables magnesium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium ion homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to ATP	IDA Inferred from Direct Assay more info	PubMed
involved_in photoreceptor cell maintenance	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytosolic calcium ion concentration	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in blood microparticle	HDA more info	PubMed
is_active_in cell periphery	IBA Inferred from Biological aspect of Ancestor more info
located_in cuticular plate	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in muscle tendon junction	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	IEA Inferred from Electronic Annotation more info
located_in photoreceptor inner segment	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor outer segment	ISS Inferred from Sequence or Structural Similarity more info
located_in sarcolemma	IEA Inferred from Electronic Annotation more info
is_active_in stereocilium	IBA Inferred from Biological aspect of Ancestor more info
located_in stereocilium	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: calcium and integrin-binding family member 2

Names: DNA-dependent protein kinase catalytic subunit-interacting protein 2

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_033006.2 RefSeqGene

Range

5090..31929

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001271888.2 → NP_001258817.1 calcium and integrin-binding family member 2 isoform 2

See identical proteins and their annotated locations for NP_001258817.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.

Source sequence(s)

AC090260

Consensus CDS

CCDS61722.1

UniProtKB/Swiss-Prot

O75838

Related

ENSP00000442459.1, ENST00000539011.5

Conserved Domains (1) summary

COG5126
Location:25 → 135

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_001271889.2 → NP_001258818.1 calcium and integrin-binding family member 2 isoform 3

See identical proteins and their annotated locations for NP_001258818.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks two alternate exons resulting in the loss of an in-frame segment in the 5' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.

Source sequence(s)

AC090260

Consensus CDS

CCDS61723.1

UniProtKB/Swiss-Prot

O75838

Related

ENSP00000453488.1, ENST00000557846.5

Conserved Domains (1) summary

COG5126
Location:19 → 129

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]
NM_001301224.2 → NP_001288153.1 calcium and integrin-binding family member 2 isoform 4

See identical proteins and their annotated locations for NP_001288153.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (4) is longer than isoform 1.

Source sequence(s)

AC090260

UniProtKB/Swiss-Prot

O75838

Conserved Domains (1) summary

cl25352
Location:69 → 183

EFh_PEF; The penta-EF hand (PEF) family
NM_006383.4 → NP_006374.1 calcium and integrin-binding family member 2 isoform 1

See identical proteins and their annotated locations for NP_006374.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AC090260

Consensus CDS

CCDS10296.1

UniProtKB/Swiss-Prot

B4DDF0, H0YM71, O75838, Q05BT6

UniProtKB/TrEMBL

Q5TZX7

Related

ENSP00000258930.3, ENST00000258930.8

Conserved Domains (1) summary

COG5126
Location:68 → 178

FRQ1; Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]

RNA

NR_125435.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC090260

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_000015.10 Reference GRCh38.p14 Primary Assembly

Range

78104606..78131535 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005254126.4 → XP_005254183.1 calcium and integrin-binding family member 2 isoform X1

See identical proteins and their annotated locations for XP_005254183.1

UniProtKB/TrEMBL

Q5TZX7

Conserved Domains (2) summary

cd00051
Location:107 → 174

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:111 → 173

EF-hand_7; EF-hand domain pair
XM_011521161.2 → XP_011519463.1 calcium and integrin-binding family member 2 isoform X3

UniProtKB/TrEMBL

H0YKC8

Related

ENSP00000452752.1, ENST00000560618.5

Conserved Domains (2) summary

cd00051
Location:64 → 131

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:68 → 130

EF-hand_7; EF-hand domain pair
XM_047432110.1 → XP_047288066.1 calcium and integrin-binding family member 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

75967162..75994101 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054377207.1 → XP_054233182.1 calcium and integrin-binding family member 2 isoform X1
XM_054377209.1 → XP_054233184.1 calcium and integrin-binding family member 2 isoform X3

UniProtKB/TrEMBL

H0YKC8
XM_054377208.1 → XP_054233183.1 calcium and integrin-binding family member 2 isoform X2