CIB2
protein-codingcalcium 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]
- DFNB48
- USH1J
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019588
Submitter: Orphanet
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.
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.
Inheritance Pattern: AR
Disease ID:MONDO:0012273
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: Unknown
Disease ID:MONDO:0013935
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013935
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0012273
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Ophthalmologic
Intervention: Audiologic/Otolaryngologic
Rationale: Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CIB2 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 48 | 50 | |||
| missense | 2 | 6 | 82 | 3 | 93 | |
| nonsense | 3 | 3 | 6 | |||
| start loss | 0 | |||||
| frameshift | 9 | 7 | 16 | |||
| splice donor/acceptor (+/-2bp) | 1 | 4 | 1 | 6 | ||
| Total | 15 | 20 | 85 | 51 | 0 | 171 |
Highest pathogenic variant AF is 0.000080677295
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006374.1 | 6 | MANE Select | |
| Ensembl | ENSP00000258930.3 | 6 | MANE Select | |
| RefSeq | NP_001258817.1 | 4 | Standard | |
| RefSeq | NP_001258818.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| cib2 | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.519 | 98 | 114 | 0.863 | 0.00000685 | 1258 |
| Missense (PolyPhen) | 26 | 35.345 | 0.7356 | 416 | ||
| Synonymous | 0.379 | 43 | 46.3 | 0.929 | 0.00000320 | 324 |
| Loss of Function | 1.37 | 6 | 10.9 | 0.553 | 6.30e-7 | 116 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00033 | 0.00033 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00049 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |