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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History.
Title: IQCB1 (NPHP5)-Retinopathy: Clinical and Genetic Characterization and Natural History.
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.
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.
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.
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.
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.
that nephrocystin-5 is essential for photoreceptor outer segment formation
Title: Ciliopathy-associated IQCB1/NPHP5 protein is required for mouse photoreceptor outer segment formation.
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.
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.
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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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	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH25274 (e-PCR)
- UniSTS:32769

IQCB1_8973 (e-PCR)
- UniSTS:468484

WI-9285 (e-PCR)
- UniSTS:12591

D6S2310 (e-PCR)
- UniSTS:6299

SHGC-77249 (e-PCR)
- UniSTS:45226

D3S2334 (e-PCR)
- UniSTS:149695

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 more info	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

NG_015887.1 RefSeqGene

Range

5020..70319

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

121769761..121835060 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017007539.3 → XP_016863028.1 IQ calmodulin-binding motif-containing protein 1 isoform X4
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
XM_047449251.1 → XP_047305207.1 IQ calmodulin-binding motif-containing protein 1 isoform X2
XM_047449250.1 → XP_047305206.1 IQ calmodulin-binding motif-containing protein 1 isoform X2
XM_047449252.1 → XP_047305208.1 IQ calmodulin-binding motif-containing protein 1 isoform X3
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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

124489717..124555054 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348484.1 → XP_054204459.1 IQ calmodulin-binding motif-containing protein 1 isoform X4
XM_054348480.1 → XP_054204455.1 IQ calmodulin-binding motif-containing protein 1 isoform X1
XM_054348482.1 → XP_054204457.1 IQ calmodulin-binding motif-containing protein 1 isoform X2
XM_054348481.1 → XP_054204456.1 IQ calmodulin-binding motif-containing protein 1 isoform X2
XM_054348483.1 → XP_054204458.1 IQ calmodulin-binding motif-containing protein 1 isoform X3
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

NM_014642.2: Suppressed sequence

Description

NM_014642.2: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.