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IQCB1 IQ motif containing B1 [ Homo sapiens (human) ]

Gene ID: 9657, updated on 27-Nov-2024

Summary

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Official Symbol
IQCB1provided by HGNC
Official Full Name
IQ motif containing B1provided by HGNC
Primary source
HGNC:HGNC:28949
See related
Ensembl:ENSG00000173226 MIM:609237; AllianceGenome:HGNC:28949
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
PIQ; NPHP5; SLSN5
Summary
This gene encodes a nephrocystin protein that interacts with calmodulin and the retinitis pigmentosa GTPase regulator protein. The encoded protein has a central coiled-coil region and two calmodulin-binding IQ domains. It is localized to the primary cilia of renal epithelial cells and connecting cilia of photoreceptor cells. The protein is thought to play a role in ciliary function. Defects in this gene result in Senior-Loken syndrome type 5. Alternative splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in testis (RPKM 16.8), lymph node (RPKM 10.7) and 25 other tissues See more
Orthologs
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Genomic context

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See IQCB1 in Genome Data Viewer
Location:
3q13.33; 3q21.1
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (121769761..121835060, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (124489717..124555054, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (121488608..121553907, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20346 Neighboring gene hematopoietic cell-specific Lyn substrate 1 Neighboring gene RNA, U4 small nuclear 62, pseudogene Neighboring gene golgin B1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:121449808-121451007 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20349 Neighboring gene ELL associated factor 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:121611674-121612207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:121612208-121612740 Neighboring gene solute carrier family 15 member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:121657363-121657943

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History. Sen S, et al. Am J Ophthalmol, 2024 Aug. PMID 38522724
  2. Clinical features and mutation of NPHP5 in two Chinese siblings with Senior-Løken syndrome. Tong H, et al. Nephrology (Carlton), 2013 Dec. PMID 24674142
  3. Requirement of NPHP5 in the hierarchical assembly of basal feet associated with basal bodies of primary cilia. Hossain D, et al. Cell Mol Life Sci, 2020 Jan. PMID 31177295, Free PMC Article
  4. Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis. le Maire A, et al. Proteins, 2005 May 1. PMID 15723349
  5. Cloning and characterization of a p53 and DNA damage down-regulated gene PIQ that codes for a novel calmodulin-binding IQ motif protein and is up-regulated in gastrointestinal cancers. Luo X, et al. Cancer Res, 2005 Dec 1. PMID 16322217

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History.
    Title: IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History.
  2. Genetic variations in the CTLA-4 immune checkpoint pathway are associated with colon cancer risk, prognosis, and immune infiltration via regulation of IQCB1 expression.
    Title: Genetic variations in the CTLA-4 immune checkpoint pathway are associated with colon cancer risk, prognosis, and immune infiltration via regulation of IQCB1 expression.
  3. SENIOR-LOKEN SYNDROME: A Case Series and Review of the Renoretinal Phenotype and Advances of Molecular Diagnosis.
    Title: SENIOR-LØKEN SYNDROME: A Case Series and Review of the Renoretinal Phenotype and Advances of Molecular Diagnosis.
  4. During ciliogenesis, the mother centriole transforms into a basal body competent to nucleate a cilium. The mother centriole and basal body possess sub-distal appendages (SDAs) and basal feet (BF), respectively. SDAs are distinguishable from BF and the protein NPHP5 is a novel SDA and BF component. NPHP5 regulates BF assembly.
    Title: Requirement of NPHP5 in the hierarchical assembly of basal feet associated with basal bodies of primary cilia.
  5. Cone vision improvement potential in LCA due to CEP290 or NPHP5 mutations is predictable from retinal structure using a machine learning approach. This should allow individual prediction of the maximal efficacy in clinical trials and guide decisions about dosing.
    Title: Treatment Potential for Macular Cone Vision in Leber Congenital Amaurosis Due to CEP290 or NPHP5 Mutations: Predictions From Artificial Intelligence.
  6. Study demonstrates the interaction between CNNM4 and IQCB1, which provides the first link between CNNM4 and IQCB1 that causes Leber congenital amaurosis and retinal dystrophy when mutated, providing important insights into the molecular pathogenic mechanisms of retinal dystrophy in Jalili syndrome.
    Title: Identification of a mutation in CNNM4 by whole exome sequencing in an Amish family and functional link between CNNM4 and IQCB1.
  7. that nephrocystin-5 is essential for photoreceptor outer segment formation
    Title: Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation.
  8. Dynamic ubiquitination and deubiquitination of NPHP5 plays a crucial role in the regulation of ciliogenesis. NPHP5 directly binds to a deubiquitinating enzyme USP9X/FAM and two E3 ubiquitin ligases BBS11/TRIM32 and MARCH7/axotrophin.
    Title: USP9X counteracts differential ubiquitination of NPHP5 by MARCH7 and BBS11 to regulate ciliogenesis.
  9. NPHP5-mutant dogs recapitulate the human phenotype of very early loss of rods, and relative retention of the central retinal cone photoreceptors that lack function.
    Title: Overlap of abnormal photoreceptor development and progressive degeneration in Leber congenital amaurosis caused by NPHP5 mutation.
  10. NPHP5 and Cep290 regulate BBSome integrity, ciliary trafficking and cargo delivery.
    Title: Nephrocystin proteins NPHP5 and Cep290 regulate BBSome integrity, ciliary trafficking and cargo delivery.
Submit: New GeneRIF Correction See all GeneRIFs (21)

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
Senior-Loken syndrome 5
MedGen: C1836517 OMIM: 609254 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables BBSome binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables calmodulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-macromolecule adaptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cilium assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in cytosolic ciliogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in maintenance of animal organ identity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in photoreceptor cell maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in centriole IEA
Inferred from Electronic Annotation
more info
  
is_active_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cilium IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in intercellular bridge IDA
Inferred from Direct Assay
more info
  
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in mitotic spindle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in photoreceptor connecting cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
IQ calmodulin-binding motif-containing protein 1
Names
nephrocystin 5
p53 and DNA damage-regulated IQ motif protein

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

  1. NG_015887.1 RefSeqGene

    Range
    5020..70319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001023570.4 → NP_001018864.2  IQ calmodulin-binding motif-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001018864.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1 and 4 encoded the same isoform (a).
    Source sequence(s)
    AC119736, AY714228, AY964668, BX393165, D25278
    Consensus CDS
    CCDS33837.1
    UniProtKB/Swiss-Prot
    Q15051, Q3KS08, Q3KS09, Q5DKQ7, Q8NI79, Q9BS08
    Related
    ENSP00000311505.6, ENST00000310864.11
    Conserved Domains (1) summary
    smart00015
    Location:387 → 408
    IQ; Calmodulin-binding motif

  2. NM_001023571.4 → NP_001018865.2  IQ calmodulin-binding motif-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001018865.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks alternate in-frame exons in the CDS, compared to variant 1. The encoded isoform (c) is shorter, compared to isoform a.
    Source sequence(s)
    AC119736, AL042102, AY964668, BC005806, BG721354, BX393165, D25278
    Consensus CDS
    CCDS33836.1
    UniProtKB/Swiss-Prot
    Q15051
    Related
    ENSP00000323756.7, ENST00000349820.10
    Conserved Domains (1) summary
    smart00015
    Location:254 → 275
    IQ; Calmodulin-binding motif

  3. NM_001319107.2 → NP_001306036.1  IQ calmodulin-binding motif-containing protein 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1 and 4 encoded the same isoform (a).
    Source sequence(s)
    AC119736, AY964668
    Consensus CDS
    CCDS33837.1
    UniProtKB/Swiss-Prot
    Q15051, Q3KS08, Q3KS09, Q5DKQ7, Q8NI79, Q9BS08
    Conserved Domains (1) summary
    smart00015
    Location:387 → 408
    IQ; Calmodulin-binding motif

RNA

  1. NR_134968.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) use alternate splice site and lacks an exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB062481, AC119736, HY195680

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    121769761..121835060 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007539.3 → XP_016863028.1  IQ calmodulin-binding motif-containing protein 1 isoform X4

  2. XM_005247911.5 → XP_005247968.1  IQ calmodulin-binding motif-containing protein 1 isoform X1

    Conserved Domains (1) summary
    smart00015
    Location:387 → 408
    IQ; Calmodulin-binding motif

  3. XM_047449251.1 → XP_047305207.1  IQ calmodulin-binding motif-containing protein 1 isoform X2

  4. XM_047449250.1 → XP_047305206.1  IQ calmodulin-binding motif-containing protein 1 isoform X2

  5. XM_047449252.1 → XP_047305208.1  IQ calmodulin-binding motif-containing protein 1 isoform X3

  6. XM_047449253.1 → XP_047305209.1  IQ calmodulin-binding motif-containing protein 1 isoform X5

    Related
    ENSP00000377261.3, ENST00000393650.7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    124489717..124555054 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348484.1 → XP_054204459.1  IQ calmodulin-binding motif-containing protein 1 isoform X4

  2. XM_054348480.1 → XP_054204455.1  IQ calmodulin-binding motif-containing protein 1 isoform X1

  3. XM_054348482.1 → XP_054204457.1  IQ calmodulin-binding motif-containing protein 1 isoform X2

  4. XM_054348481.1 → XP_054204456.1  IQ calmodulin-binding motif-containing protein 1 isoform X2

  5. XM_054348483.1 → XP_054204458.1  IQ calmodulin-binding motif-containing protein 1 isoform X3

  6. XM_054348485.1 → XP_054204460.1  IQ calmodulin-binding motif-containing protein 1 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014642.2: Suppressed sequence

    Description
    NM_014642.2: This RefSeq record was removed by NCBI staff. Contact [email protected] for further information.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15051.1 GenPept UniProtKB/Swiss-Prot:Q15051

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