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GeneBe

CCDC39

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

Basic information

Region (hg38): 3:180602857-180684942

Links

ENSG00000284862 ∙ NCBI:339829 ∙ OMIM:613798 ∙ HGNC:25244 ∙ Uniprot:Q9UFE4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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 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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ciliary dyskinesia, primary, 14ARAllergy/Immunology/Infectious; Audiologic/Otolaryngologic; PulmonaryPulmonary 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 managementAllergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary20301301; 21131972

ClinVar

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

  • Primary ciliary dyskinesia (494 variants)
  • Primary ciliary dyskinesia 14 (141 variants)
  • not provided (91 variants)
  • not specified (47 variants)
  • Inborn genetic diseases (19 variants)
  • CCDC39-related condition (3 variants)
  • Ellis-van Creveld syndrome (1 variants)
  • Heterotaxy (1 variants)
  • Infertility disorder (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.

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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
2
clinvar
98
clinvar
4
clinvar
 104
missense
153
clinvar
11
clinvar
5
clinvar
 169
nonsense
28
clinvar
3
clinvar
 31
start loss
0
frameshift
51
clinvar
4
clinvar
1
clinvar
1
clinvar
 57
inframe indel
1
clinvar
4
clinvar
 5
splice donor/acceptor (+/-2bp)
8
clinvar
8
clinvar
1
clinvar
 17
splice region
?
    Intron variants in splice region, excluding donor/acceptor (+/-2bp)
13
13
1
 27
non coding
?
    UTR, intron and other, non coding variants
3
clinvar
35
clinvar
70
clinvar
42
clinvar
 150
Total 87 19 196 180 51

Highest pathogenic variant AF is 0.0000854

Variants in CCDC39

This is a list of pathogenic ClinVar variants found in the CCDC39 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
3-180602910-A-G not specified Uncertain significance (Jun 13, 2023)2559944
3-180602935-C-T not specified Uncertain significance (Apr 07, 2022)2205018
3-180602983-C-T not specified Uncertain significance (Sep 14, 2022)2370433
3-180602997-A-C not specified Uncertain significance (Dec 20, 2023)3184083
3-180603009-A-G not specified Uncertain significance (Oct 26, 2021)2226235
3-180603109-A-AT TTC14-related disorder Benign (Sep 23, 2019)3059709
3-180603130-A-G not specified Uncertain significance (Nov 10, 2022)2343209
3-180603174-A-G not specified Uncertain significance (Dec 08, 2023)3184084
3-180603199-G-A not specified Uncertain significance (Dec 19, 2022)2337016
3-180603243-A-G not specified Uncertain significance (Nov 10, 2022)2323226
3-180603295-T-A not specified Uncertain significance (Dec 17, 2023)3184085
3-180603306-G-A not specified Uncertain significance (Dec 06, 2023)3184086
3-180604857-G-A not specified Uncertain significance (May 03, 2023)2522669
3-180604857-G-C not specified Uncertain significance (Oct 25, 2022)2319056
3-180604940-G-C not specified Uncertain significance (Mar 03, 2022)2396852
3-180604953-A-G not specified Likely benign (Aug 09, 2021)2376324
3-180605796-T-C TTC14-related disorder Benign (Jul 12, 2019)3050662
3-180606262-C-T TTC14-related disorder Likely benign (Nov 21, 2019)3048566
3-180606487-G-A TTC14-related disorder Benign (Sep 18, 2019)3038263
3-180606574-C-T TTC14-related disorder Likely benign (Aug 12, 2019)3035715
3-180606587-G-A not specified Uncertain significance (Jan 29, 2024)3184078
3-180608750-A-C not specified Uncertain significance (Apr 14, 2022)2254213
3-180608773-G-A not specified Uncertain significance (May 25, 2022)2290954
3-180609668-G-A not specified Uncertain significance (Dec 19, 2022)3184079
3-180609742-C-T TTC14-related disorder Likely benign (Aug 21, 2022)3045653

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP