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CCDC28B coiled-coil domain containing 28B [ Homo sapiens (human) ]

Gene ID: 79140, updated on 3-Apr-2024

Summary

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Official Symbol
CCDC28Bprovided by HGNC
Official Full Name
coiled-coil domain containing 28Bprovided by HGNC
Primary source
HGNC:HGNC:28163
See related
Ensembl:ENSG00000160050 MIM:610162; AllianceGenome:HGNC:28163
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
Summary
The product of this gene localizes to centrosomes and basal bodies. The protein colocalizes with several proteins associated with Bardet-Biedl syndrome (BBS) and participates in the regulation of cilia development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Broad expression in testis (RPKM 4.7), lymph node (RPKM 2.1) and 23 other tissues See more
Orthologs
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Genomic context

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Location:
1p35.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32196011..32205387)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32058497..32063289)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32666196..32670988)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 39B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32557367-32557892 Neighboring gene microRNA 5585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32573351-32573869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32573870-32574387 Neighboring gene Sharpr-MPRA regulatory region 5670 Neighboring gene karyopherin subunit alpha 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32644454-32645213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32645214-32645972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 670 Neighboring gene taxilin alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32664855-32665413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32665414-32665971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 672 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr1:32666522-32667041 and GRCh37_chr1:32667042-32667562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32670259-32670760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 675 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:32681346-32682545 Neighboring gene doublecortin domain containing 2B Neighboring gene IQ motif containing C Neighboring gene transmembrane protein 234

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. A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly. Capitani N, et al. Cell Death Differ, 2022 Jan. PMID 34294890, Free PMC Article
  2. The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex. Cardenas-Rodriguez M, et al. Hum Mol Genet, 2013 Oct 15. PMID 23727834, Free PMC Article
  3. Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B. Novas R, et al. Sci Rep, 2018 Feb 14. PMID 29445114, Free PMC Article
  4. BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population. Bin J, et al. Hum Mutat, 2009 Jul. PMID 19402160
  5. Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome. Cardenas-Rodriguez M, et al. Hum Genet, 2013 Jan. PMID 23015189

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly.
    Title: A CVID-associated variant in the ciliogenesis protein CCDC28B disrupts immune synapse assembly.
  2. these studies demonstrate that kinesin 1 regulates ciliogenesis through CCDC28B
    Title: Kinesin 1 regulates cilia length through an interaction with the Bardet-Biedl syndrome related protein CCDC28B.
  3. Findings implicate CCDC28B in the regulation of mTORC2, and uncover a novel function of SIN1 regulating cilia length that is likely independent of mTOR signaling.
    Title: The Bardet-Biedl syndrome-related protein CCDC28B modulates mTORC2 function and interacts with SIN1 to control cilia length independently of the mTOR complex.
  4. reports CCDC28B as a novel protein involved in the process of ciliogenesis whilst providing functional insight into the cellular basis of its modifier effect in Bardet-Biedl syndrome.
    Title: Characterization of CCDC28B reveals its role in ciliogenesis and provides insight to understand its modifier effect on Bardet-Biedl syndrome.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: BBS7 and TTC8 (BBS8) mutations play a minor role in the mutational load of Bardet-Biedl syndrome in a multiethnic population.
  6. identification of a novel locus, MGC1203, that contributes epistatic alleles to Bardet-Biedl syndrome, a pleiotropic, oligogenic disorder; MGC1203 encodes a pericentriolar protein that interacts and colocalizes with the BBS proteins
    Title: Dissection of epistasis in oligogenic Bardet-Biedl syndrome.
Submit: New GeneRIF Correction

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
Bardet-Biedl syndrome 1
MedGen: C2936862 OMIM: 209900 GeneReviews: Bardet-Biedl Syndrome Overview
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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)

Genotypes

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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Homology

Clone Names

  • MGC1203, MGC16441

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cilium assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in centrosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
coiled-coil domain-containing protein 28B

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_012178.1 RefSeqGene

    Range
    4995..9787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301011.2 → NP_001287940.1  coiled-coil domain-containing protein 28B isoform 1

    See identical proteins and their annotated locations for NP_001287940.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK291904, BC002462
    Consensus CDS
    CCDS72749.1
    UniProtKB/Swiss-Prot
    Q9BUN5
    Related
    ENSP00000413017.2, ENST00000421922.6
    Conserved Domains (1) summary
    pfam13270
    Location:86 → 183
    DUF4061; Domain of unknown function (DUF4061)

  2. NM_024296.5 → NP_077272.2  coiled-coil domain-containing protein 28B isoform 2

    See identical proteins and their annotated locations for NP_077272.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate segment in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK291904, BC022848
    Consensus CDS
    CCDS354.2
    UniProtKB/Swiss-Prot
    A8K789, Q8TBV8, Q9BUN5
    Related
    ENSP00000362704.5, ENST00000373602.10
    Conserved Domains (1) summary
    pfam13270
    Location:86 → 184
    DUF4061; Domain of unknown function (DUF4061)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    32196011..32205387
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047430215.1 → XP_047286171.1  coiled-coil domain-containing protein 28B isoform X1

  2. XM_047430217.1 → XP_047286173.1  coiled-coil domain-containing protein 28B isoform X2

    UniProtKB/Swiss-Prot
    A8K789, Q8TBV8, Q9BUN5

  3. XM_017002308.3 → XP_016857797.1  coiled-coil domain-containing protein 28B isoform X3

    UniProtKB/TrEMBL
    A0A7P0TB33, E9PM81
    Related
    ENSP00000506476.1, ENST00000681230.1
    Conserved Domains (1) summary
    pfam13270
    Location:86 → 110
    DUF4061; Domain of unknown function (DUF4061)

  4. XM_011542113.4 → XP_011540415.1  coiled-coil domain-containing protein 28B isoform X1

    See identical proteins and their annotated locations for XP_011540415.1

    UniProtKB/Swiss-Prot
    Q9BUN5
    Conserved Domains (1) summary
    pfam13270
    Location:86 → 183
    DUF4061; Domain of unknown function (DUF4061)

  5. XM_017002307.2 → XP_016857796.1  coiled-coil domain-containing protein 28B isoform X2

    UniProtKB/Swiss-Prot
    A8K789, Q8TBV8, Q9BUN5
    Conserved Domains (1) summary
    pfam13270
    Location:86 → 184
    DUF4061; Domain of unknown function (DUF4061)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    32058497..32063289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338690.1 → XP_054194665.1  coiled-coil domain-containing protein 28B isoform X3

    UniProtKB/TrEMBL
    A0A7P0TB33

  2. XM_054338687.1 → XP_054194662.1  coiled-coil domain-containing protein 28B isoform X1

  3. XM_054338688.1 → XP_054194663.1  coiled-coil domain-containing protein 28B isoform X1

  4. XM_054338689.1 → XP_054194664.1  coiled-coil domain-containing protein 28B isoform X2

    UniProtKB/Swiss-Prot
    A8K789, Q8TBV8, Q9BUN5
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BUN5.2 GenPept UniProtKB/Swiss-Prot:Q9BUN5

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