CCDC39 coiled-coil domain 39 molecular ruler complex subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCDC39provided by HGNC
Official Full Name: coiled-coil domain 39 molecular ruler complex subunitprovided by HGNC
Primary source: HGNC:HGNC:25244
See related: Ensembl:ENSG00000284862 MIM:613798; AllianceGenome:HGNC:25244
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FAP59; CFAP59; CILD14
Summary: The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
Expression: Broad expression in testis (RPKM 5.3), lymph node (RPKM 2.5) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q26.33

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (180614008..180679489, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (183415869..183481362, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (180331796..180397277, 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:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Primary Ciliary Dyskinesia Associated Disease-Causing Variants in CCDC39 and CCDC40 Cause Axonemal Absence of Inner Dynein Arm Heavy Chains DNAH1, DNAH6, and DNAH7.
Title: Primary Ciliary Dyskinesia Associated Disease-Causing Variants in CCDC39 and CCDC40 Cause Axonemal Absence of Inner Dynein Arm Heavy Chains DNAH1, DNAH6, and DNAH7.
Biallelic Variants in CCDC39 Gene Lead to Primary Ciliary Dyskinesia and Kartagener Syndrome.
Title: Biallelic Variants in CCDC39 Gene Lead to Primary Ciliary Dyskinesia and Kartagener Syndrome.
A novel CCDC39 mutation causes multiple morphological abnormalities of the flagella in a primary ciliary dyskinesia patient.
Title: A novel CCDC39 mutation causes multiple morphological abnormalities of the flagella in a primary ciliary dyskinesia patient.
Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia.
Title: Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia.
Deep phenotyping, including quantitative ciliary beating parameters, and extensive genotyping in primary ciliary dyskinesia.
Title: Deep phenotyping, including quantitative ciliary beating parameters, and extensive genotyping in primary ciliary dyskinesia.
Lung disease was worse in those with IDA/CA/MTD ultrastructural defects, most of whom had biallelic mutations in ccdc39.
Title: Clinical features of childhood primary ciliary dyskinesia by genotype and ultrastructural phenotype.
This study shows that CCDC39 and CCDC40 mutations are the major cause of Primary ciliary dyskinesia in patients with the previously termed "radial spoke defect".
Title: Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms.
Aiming to delineate the CCDC39/CCDC40 mutation spectrum and associated phenotypes, a large cohort of patients with IDA defects were screened. Biallelic CCDC39 or CCDC40 mutations were identified in 30/34 unrelated families with IDA defects.
Title: Delineation of CCDC39/CCDC40 mutation spectrum and associated phenotypes in primary ciliary dyskinesia.
Functional analyses indicated that CCDC39 localizes to ciliary axonemes and is essential for assembly of inner dynein arms and the dynein regulatory complex.
Title: CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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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
Primary ciliary dyskinesia 14 MedGen: C3151136 OMIM: 613807 GeneReviews: Primary Ciliary Dyskinesia	not available

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

WI-11544 (e-PCR)
- UniSTS:21291

RH66248 (e-PCR)
- UniSTS:1074

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in axonemal dynein complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain development	IEA Inferred from Electronic Annotation more info
involved_in cerebrospinal fluid circulation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cilium movement	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium-dependent cell motility	IBA Inferred from Biological aspect of Ancestor more info
involved_in cilium-dependent cell motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of digestive tract left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of liver left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of pancreatic left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial cilium movement involved in determination of left/right asymmetry	IBA Inferred from Biological aspect of Ancestor more info
involved_in epithelial cilium movement involved in determination of left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of left/right asymmetry	IEA Inferred from Electronic Annotation more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within flagellated sperm motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inner dynein arm assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner dynein arm assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lung development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within motile cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein localization to cilium	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cilium beat frequency	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in axoneme	IBA Inferred from Biological aspect of Ancestor more info
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: coiled-coil domain-containing protein 39

Names: coiled-coil domain containing 39

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_029581.1 RefSeqGene

Range

5007..70488

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_181426.2 → NP_852091.1 coiled-coil domain-containing protein 39

See identical proteins and their annotated locations for NP_852091.1

Status: VALIDATED

Source sequence(s)

AL122120, BG205877, DC399927

Consensus CDS

CCDS46964.1

UniProtKB/Swiss-Prot

B4E2H1, Q9UFE4

UniProtKB/TrEMBL

A0A494C1Q3

Related

ENSP00000417960.2, ENST00000476379.6

Conserved Domains (1) summary

COG1196
Location:22 → 848

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]