CCDC39

coiled-coil domain containing 39, the group of Cilia and flagella associated

Basic information

Region (hg38): 3:180602858-180684942

Links

∙ NCBI:339829 ∙ OMIM:613798 ∙ HGNC:25244 ∙ Uniprot:Q9UFE4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
`NM_181426.2`	`NP_852091.1`	20	yes	-
`ENST00000476379.6`	`ENSP00000417960.2`	20	yes	-
`ENST00000473854.5`	`ENSP00000418482.1`	4	-	-
`ENST00000489868.6`	`ENSP00000420025.1`	3	-	-

Phenotypes

GenCC

Source: genCC

primary ciliary dyskinesia 14 (Definitive), mode of inheritance: AR
primary ciliary dyskinesia 14 (Strong), mode of inheritance: AR
primary ciliary dyskinesia (Supportive), mode of inheritance: AD
primary ciliary dyskinesia 14 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 14	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Pulmonary	Pulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing function and institute early management measures; In order to facilitate mucus clearance, aggressive interventions (eg, chest percussion and oscillatory vest), as well as vaccinations and early and aggressive treatment of respiratory infections may be beneficial, though measures including lobectomy or lung transplantation may be necessary; Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary	20301301; 21131972

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ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CCDC39 gene.

Primary_ciliary_dyskinesia (828 variants)
Primary_ciliary_dyskinesia_14 (147 variants)
not_provided (74 variants)
not_specified (41 variants)
CCDC39-related_disorder (21 variants)
Respiratory_ciliopathies_including_non-CF_bronchiectasis (3 variants)
Ellis-van_Creveld_syndrome (1 variants)
Infertility_disorder (1 variants)
Heterotaxy (1 variants)
Fibrous_Sheath_Dysplasia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CCDC39 gene is commonly pathogenic or not. These statistics are base on transcript: NM_181426.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar	1 clinvar	2 clinvar	213 clinvar	1 clinvar	218
missense	1 clinvar	3 clinvar	231 clinvar	31 clinvar	5 clinvar	271
nonsense	40 clinvar	11 clinvar				51
start loss		1				1
frameshift	68 clinvar	22 clinvar		1 clinvar		91
splice donor/acceptor (+/-2bp)	12 clinvar	18 clinvar	3 clinvar			33
Total	122	56	236	245	6

Highest pathogenic variant AF is 0.0004661974

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GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP