CCDC40 coiled-coil domain 40 molecular ruler complex subunit [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCDC40provided by HGNC
Official Full Name: coiled-coil domain 40 molecular ruler complex subunitprovided by HGNC
Primary source: HGNC:HGNC:26090
See related: Ensembl:ENSG00000141519 MIM:613799; AllianceGenome:HGNC:26090
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: CILD15; FAP172; CFAP172
Summary: This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression: Broad expression in testis (RPKM 4.5), lung (RPKM 1.1) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q25.3

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (80036642..80100613)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (80935298..81001052)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (78010441..78074412)

Chromosome 17 - NC_000017.11 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: 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?

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.
CCDC40 mutation as a cause of infertility in a Chinese family with primary ciliary dyskinesia.
Title: CCDC40 mutation as a cause of infertility in a Chinese family with primary ciliary dyskinesia.
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.
A novel mutation causing primary ciliary dyskinesia was found in Japanese patients.
Title: A targeted next-generation sequencing panel reveals novel mutations in Japanese patients with primary ciliary dyskinesia.
Results identified a novel mutant alleles in CCDC40 gene, which altered the protein sequence and resulted in the ultrastructural defects in the microtubule structure of cilia suggesting that CCDC40 mutation may be a cause for ciliary dyskinesia.
Title: CCDC40 mutation as a cause of primary ciliary dyskinesia: a case report and review of literature.
Lung disease was worse in those with IDA/CA/MTD ultrastructural defects, most of whom had biallelic mutations in ccdc40.
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.
CCDC40 mutations in humans result in a variant of primary ciliary dyskinesia characterized by misplacement of the central pair of microtubules and defective assembly of inner dynein arms and dynein regulatory complexes.
Title: The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation.

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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 15 MedGen: C3151137 OMIM: 613808 GeneReviews: Primary Ciliary Dyskinesia	Compare labs

EBI GWAS Catalog

Description
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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

D11S2921 (e-PCR)
- UniSTS:152074

RH98689 (e-PCR)
- UniSTS:88075

SHGC-58932 (e-PCR)
- UniSTS:94481

RH92754 (e-PCR)
- UniSTS:83730

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in axonemal dynein complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axoneme assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cilium movement	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 epithelial cilium movement involved in extracellular fluid movement	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within flagellated sperm motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart looping	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within regulation of cilium beat frequency	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cilium beat frequency	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in axoneme	IDA Inferred from Direct Assay more info	PubMed
is_active_in cilium	IBA Inferred from Biological aspect of Ancestor more info
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISS Inferred from Sequence or Structural Similarity more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity 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 40

Names: coiled-coil domain containing 40

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_029761.1 RefSeqGene

Range

5011..68982

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001243342.2 → NP_001230271.1 coiled-coil domain-containing protein 40 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.

Source sequence(s)

AB046860, AC087741, BC035251, BQ009577, DA842356, DB230102

Consensus CDS

CCDS58604.1

UniProtKB/Swiss-Prot

Q4G0X9

Related

ENSP00000364011.3, ENST00000374877.7

Conserved Domains (2) summary

TIGR02168
Location:239 → 934

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam08647
Location:780 → 878

BRE1; BRE1 E3 ubiquitin ligase
NM_001330508.2 → NP_001317437.1 coiled-coil domain-containing protein 40 isoform 3

Status: REVIEWED

Source sequence(s)

AC116025

Consensus CDS

CCDS82212.1

UniProtKB/Swiss-Prot

Q4G0X9

Related

ENSP00000269318.5, ENST00000269318.9
NM_017950.4 → NP_060420.2 coiled-coil domain-containing protein 40 isoform 1

See identical proteins and their annotated locations for NP_060420.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). There are no publicly available full-length transcripts representing this variant, but it is supported by partial transcript alignments and by data in PMID:21131974.

Source sequence(s)

AB046860, AW300891, BC035251, DA842356, DB230102

Consensus CDS

CCDS42395.1

UniProtKB/Swiss-Prot

A8MTD2, C9JTI9, C9JTJ0, C9JXW1, J3QSY2, Q4G0X9, Q6PE47, Q9HCD2, Q9NWL5

Related

ENSP00000380679.4, ENST00000397545.9

Conserved Domains (2) summary

COG1196
Location:295 → 1129

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

pfam08647
Location:780 → 878

BRE1; BRE1 E3 ubiquitin ligase