CIB2

protein-coding

calcium and integrin binding family member 2, the group of EF-hand domain containing

Gene 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]

Previous symbols:
  • DFNB48
  • USH1J

MANE transcript

NM_006383.4

Inheritance

AR

ClinVar variants

P:35U:85B:51

Top phenotype

Deafness, autosomal recessive 48; Usher syndrome type IJ

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr15:78,104,606-78,131,535

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hearing loss, autosomal recessiveSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019588

Submitter: Orphanet

Usher syndrome type 1NO_KNOWN

Inheritance Pattern: AR

Disease ID:MONDO:0010168

Submitter: ClinGen

CIB2 was first reported in relation to autosomal recessive Usher syndrome Type 1 in 2012 (Riazuddin et al., 23023331). One homozygous missense variants in this gene has been reported in at least one proband in one publication (Riazuddin et al. 2012, 23023331). Variants in this gene segregated with disease in 3 additional family members. One additional missense variant has been reported in heterozygosity in an affected individual, however the variant is frequent in population databases and no second pathogenic variant was identified (Fuster-Garcia et al. 2018, 30459346). Booth et al. 2017 (29112224) studied a multi-ethnic cohort of patients with CIB2-related-ARNSHL. All patients in this study have normal ocular phenotype and no vestibular dysfunction regardless of the variant impact. Booth et al. 2017 note that the p.Glu64Asp variant in the Riazuddin Usher family is only two amino acids away from the p.Arg66Trp variant that has been linked to ARNSHL in three families. Booth et al. argue that if CIB2 played a role in Usher syndrome, we would expect to see a retinal and vestibular phenotype in families segregating LOF variants. Michel et al. 2017 (29084757) described 2 families with CIB2-related-ARNSHL. Both families segregate LOF variants and have normal eye phneotype with no pigment deposits. In addition to the variants reported by Booth and Michel, 7 other variants have been linked solely to CIB2-related-ARNSHL (see the CIB2 and ARNSHL gene-disease pair). Michel et al. 2017 also described a CIB2 knockout mouse model. This mouse model displayed congenital profound deafness with no vestibular defect. It also exhibited normal cochlear hair bundle architecture up to postnatal day 7. This is in contrast with all other known USH1 mouse models, which display severe vestibular dysfunction and abnormal cochlear hair bundle architecture starting around postnatal day 3. Other CIB2-murine mutants (28663585 and 29255404) display an identical phenotype to that described by Michel et al. Additionally, it was shown that loss of known USH proteins like MYO7A, PCDH15, USH1C, WHRN, USH2A and PDZD7 does not affect the localization of CIB2, and vice versa. In summary, there is convincing evidence refuting the relationship between CIB2 and autosomal recessive Usher syndrome Type 1, which significantly outweighs the evidence supporting the relationship. This classification was approved by the ClinGen Hearing Loss Working Group on 02/19/2019.

nonsyndromic genetic hearing lossDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019497

Submitter: ClinGen

The CIB2 gene has been associated with autosomal recessive nonsyndromic hearing loss using the ClinGen Clinical Validity Framework as of 10/19/2017. This association was made using case-level data only. At least 9 variants (missense, in-frame indel, nonsense, frameshift) have been reported in humans. CIB2 was first associated with this disease in humans as early as 2012 (Riazuddin et al.). Association is seen in at least 9 probands in 6 publications (23023331, 26173970, 26473954, 27344577, 26226137, 26445815). Variants in this gene segregated with disease in 4 additional family members. More evidence is available in the literature, but the maximum score for genetic evidence and experimental evidence have been reached. This gene-disease association is supported by two mouse models (Giese et al. 2017) and a zebrafish model (Riazuddin et al. 2012). In summary, CIB2 is definitively associated with autosomal recessive nonsyndromic hearing loss. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen Hearing Loss Working Group on 2/20/2018.

autosomal recessive nonsyndromic hearing loss 48STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012273

Submitter: Labcorp Genetics (formerly Invitae)

Usher syndrome type 1JLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013935

Submitter: Labcorp Genetics (formerly Invitae)

Usher syndrome type 1JDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013935

Submitter: G2P

autosomal recessive nonsyndromic hearing loss 48STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012273

Submitter: G2P

Clinical Genomic Database (CGD)

Deafness, autosomal recessive 48; Usher syndrome type IJAR

Manifestation: Audiologic/Otolaryngologic; Ophthalmologic

Intervention: Audiologic/Otolaryngologic

Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development

Refs: 18505454; 23023331Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CIB2 variants in ClinVar

13 Conditions Cataloged
not providedTotal: 191
not specifiedTotal: 40
Autosomal recessive nonsyndromic hearing loss 48Total: 28
Inborn genetic diseasesTotal: 21
CIB2-related disorderTotal: 15
CIB2-related disordersTotal: 11
Retinal dystrophyTotal: 3
Hearing loss, autosomal recessiveTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006383.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
48
clinvar
50
missense
2
clinvar
6
clinvar
82
clinvar
3
clinvar
93
nonsense
3
clinvar
3
clinvar
6
start loss
0
frameshift
9
clinvar
7
clinvar
16
splice donor/acceptor (+/-2bp)
1
clinvar
4
clinvar
1
clinvar
6
Total152085510171

Highest pathogenic variant AF is 0.000080677295

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006383.4RefSeqNP_006374.16MANE Select
ENST00000258930.8EnsemblENSP00000258930.36MANE Select
NM_001271888.2RefSeqNP_001258817.14Standard
NM_001271889.2RefSeqNP_001258818.14Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
cib2Danio rerio

Structure: neuromast hair cell

Quality: mislocalised

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • positive regulation of cytosolic calcium ion concentration
  • photoreceptor cell maintenance
  • calcium ion homeostasis
  • cellular response to ATP

Molecular Function

  • magnesium ion binding
  • integrin binding
  • calcium ion binding
  • protein binding
  • protein homodimerization activity

Cellular Component

  • photoreceptor outer segment
  • photoreceptor inner segment
  • cytoplasm
  • muscle tendon junction
  • neuromuscular junction

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000258930
Coding exons
6
Length
26939
Individuals with no LoFs
125706
Homozygous LoFs
0
Heterozygous LoFs
42
Defined
125748
p
0.000167
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.519981140.8630.000006851258
Missense (PolyPhen)2635.3450.7356416
Synonymous0.3794346.30.9290.00000320324
Loss of Function1.37610.90.5536.30e-7116

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.000330.00033rare
South Asian0.0000330.000033rare
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Calcium-binding protein critical for proper photoreceptor cell maintenance and function. Plays a role in intracellular calcium homeostasis by decreasing ATP-induced calcium release (PubMed:23023331, PubMed:26173970, PubMed:26426422). May be involved in the mechanotransduction process (By similarity). {ECO:0000250, ECO:0000269|PubMed:23023331, ECO:0000269|PubMed:26173970, ECO:0000269|PubMed:26426422}.;
Disease
DISEASE: Usher syndrome 1J (USH1J) [MIM:614869]: USH is a genetically heterogeneous condition characterized by the association of retinitis pigmentosa with sensorineural deafness. Age at onset and differences in auditory and vestibular function distinguish Usher syndrome type 1 (USH1), Usher syndrome type 2 (USH2) and Usher syndrome type 3 (USH3). USH1 is characterized by profound congenital sensorineural deafness, absent vestibular function and prepubertal onset of progressive retinitis pigmentosa leading to blindness. {ECO:0000269|PubMed:23023331}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.136

Intolerance Scores

LoFtool
0.623
RVIS EVS
-0.29
RVIS percentile EVS
32.94

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.577

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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