IQCB1

IQ motif containing B1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:121769761-121835079

Links

ENSG00000173226

∙ NCBI:9657 ∙ OMIM:609237 ∙ HGNC:28949 ∙ Uniprot:Q15051 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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
Senior-Loken syndrome 5 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the IQCB1 gene.

Nephronophthisis (383 variants)
Senior-Loken_syndrome_5 (199 variants)
not_provided (63 variants)
Inborn_genetic_diseases (52 variants)
IQCB1-related_disorder (19 variants)
Retinal_dystrophy (13 variants)
Leber_congenital_amaurosis (7 variants)
not_specified (7 variants)
Renal_dysplasia_and_retinal_aplasia (5 variants)
Retinitis_pigmentosa (2 variants)
Bardet-Biedl_syndrome (1 variants)
See_cases (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. These statistics are base on transcript: NM_001023570.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				76 clinvar		76
missense		1 clinvar	229 clinvar	12 clinvar	2 clinvar	244
nonsense	25 clinvar	13 clinvar	3 clinvar			41
start loss						0
frameshift	21 clinvar	14 clinvar	2 clinvar			37
splice donor/acceptor (+/-2bp)	2 clinvar	17 clinvar	2 clinvar			21
Total	48	45	236	88	2

Highest pathogenic variant AF is 0.000185238

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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