IQCB1
Basic information
Region (hg38): 3:121769761-121835079
Links
Phenotypes
GenCC
Source:
- Senior-Loken syndrome (Supportive), mode of inheritance: AR
- Leber congenital amaurosis (Supportive), mode of inheritance: AD
- Senior-Loken syndrome 5 (Strong), mode of inheritance: AR
- Leber congenital amaurosis 9 (Definitive), mode of inheritance: AR
- Senior-Loken syndrome 5 (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Senior-Loken syndrome 5 | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Ophthalmologic; Renal | 15723066; 21220633; 23661368 |
ClinVar
This is a list of variants' phenotypes submitted to
- Nephronophthisis (30 variants)
- Senior-Loken syndrome 5 (25 variants)
- not provided (11 variants)
- Retinal dystrophy (6 variants)
- Leber congenital amaurosis (5 variants)
- Renal dysplasia and retinal aplasia (2 variants)
- Retinitis pigmentosa (1 variants)
- IQCB1-related disorder (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCB1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 61 | 63 | ||||
missense | 178 | 186 | ||||
nonsense | 23 | 34 | ||||
start loss | 0 | |||||
frameshift | 15 | 13 | 29 | |||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 13 | 16 | ||||
splice region | 13 | 13 | 2 | 28 | ||
non coding | 15 | 71 | 48 | 135 | ||
Total | 42 | 34 | 199 | 137 | 52 |
Highest pathogenic variant AF is 0.000126
Variants in IQCB1
This is a list of pathogenic ClinVar variants found in the IQCB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
3-121769946-T-C | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770018-A-G | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770119-A-G | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770127-C-T | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770148-C-G | Senior-Loken syndrome 5 | Benign (Nov 12, 2018) | ||
3-121770185-G-A | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770194-A-G | Senior-Loken syndrome 5 | Uncertain significance (Jan 13, 2018) | ||
3-121770197-A-G | Senior-Loken syndrome 5 | Uncertain significance (Jan 13, 2018) | ||
3-121770373-A-C | Nephronophthisis | Uncertain significance (Jan 13, 2021) | ||
3-121770379-T-G | Inborn genetic diseases | Uncertain significance (Sep 27, 2021) | ||
3-121770390-A-G | Nephronophthisis | Likely benign (Nov 28, 2022) | ||
3-121770391-C-T | Nephronophthisis | Uncertain significance (May 08, 2023) | ||
3-121770396-C-T | Nephronophthisis • IQCB1-related disorder | Likely benign (Dec 30, 2023) | ||
3-121770401-C-G | Nephronophthisis • Senior-Loken syndrome 5 | Uncertain significance (Feb 03, 2022) | ||
3-121770403-T-G | Senior-Loken syndrome 5 | Uncertain significance (Jan 12, 2018) | ||
3-121770404-T-G | Nephronophthisis | Uncertain significance (Feb 10, 2022) | ||
3-121770415-A-G | Nephronophthisis • Senior-Loken syndrome 5 | Uncertain significance (Jul 26, 2022) | ||
3-121770422-C-T | Nephronophthisis | Uncertain significance (Mar 04, 2022) | ||
3-121770431-C-A | Nephronophthisis | Uncertain significance (Feb 08, 2022) | ||
3-121770435-T-A | Nephronophthisis | Likely benign (Mar 13, 2022) | ||
3-121770436-C-G | Nephronophthisis | Uncertain significance (Jun 07, 2022) | ||
3-121770439-A-G | Nephronophthisis • IQCB1-related disorder | Conflicting classifications of pathogenicity (Apr 15, 2024) | ||
3-121770453-G-A | Nephronophthisis | Likely benign (Sep 11, 2020) | ||
3-121770454-G-C | Nephronophthisis | Uncertain significance (Jul 18, 2021) | ||
3-121770455-G-C | Nephronophthisis | Uncertain significance (Jan 22, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IQCB1 | protein_coding | protein_coding | ENST00000310864 | 13 | 65317 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.36e-12 | 0.923 | 125583 | 0 | 165 | 125748 | 0.000656 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.309 | 280 | 295 | 0.949 | 0.0000143 | 3898 |
Missense in Polyphen | 72 | 85.466 | 0.84244 | 1208 | ||
Synonymous | 0.996 | 91 | 104 | 0.876 | 0.00000480 | 1118 |
Loss of Function | 2.07 | 25 | 38.9 | 0.642 | 0.00000241 | 432 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000696 | 0.000695 |
Ashkenazi Jewish | 0.00149 | 0.00149 |
East Asian | 0.000925 | 0.000925 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000908 | 0.000906 |
Middle Eastern | 0.000925 | 0.000925 |
South Asian | 0.000298 | 0.000294 |
Other | 0.000816 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in ciliogenesis. The function in an early step in cilia formation depends on its association with CEP290/NPHP6 (PubMed:21565611, PubMed:23446637). Involved in regulation of the BBSome complex integrity, specifically for presence of BBS2 and BBS5 in the complex, and in ciliary targeting of selected BBSome cargos. May play a role in controlling entry of the BBSome complex to cilia possibly implicating CEP290/NPHP6 (PubMed:25552655). {ECO:0000269|PubMed:23446637, ECO:0000269|PubMed:25552655}.;
- Disease
- DISEASE: Senior-Loken syndrome 5 (SLSN5) [MIM:609254]: A renal- retinal disorder characterized by progressive wasting of the filtering unit of the kidney (nephronophthisis), with or without medullary cystic renal disease, and progressive eye disease. Typically this disorder becomes apparent during the first year of life. {ECO:0000269|PubMed:15723066}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Leber congenital amaurosis 10 (LCA10) [MIM:611755]: A severe dystrophy of the retina, typically becoming evident in the first years of life. Visual function is usually poor and often accompanied by nystagmus, sluggish or near-absent pupillary responses, photophobia, high hyperopia and keratoconus. {ECO:0000269|PubMed:23446637}. Note=The gene represented in this entry may be involved in disease pathogenesis.;
- Pathway
- Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.176
Intolerance Scores
- loftool
- 0.985
- rvis_EVS
- 0.6
- rvis_percentile_EVS
- 82.78
Haploinsufficiency Scores
- pHI
- 0.170
- hipred
- Y
- hipred_score
- 0.607
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0000268
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Iqcb1
- Phenotype
Zebrafish Information Network
- Gene name
- iqcb1
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- curved ventral
Gene ontology
- Biological process
- photoreceptor cell maintenance;maintenance of animal organ identity;cilium assembly;ciliary basal body-plasma membrane docking
- Cellular component
- photoreceptor outer segment;nucleoplasm;centrosome;centriole;cytosol;microtubule cytoskeleton;photoreceptor connecting cilium;intercellular bridge;extracellular exosome;mitotic spindle
- Molecular function
- protein binding;calmodulin binding;enzyme binding