ODAD1

outer dynein arm docking complex subunit 1, the group of Outer dynein arm docking complex subunits

Basic information

Region (hg38): 19:48296456-48321971

Previous symbols: [ "CCDC114" ]

Links

ENSG00000105479 ∙ NCBI:93233 ∙ OMIM:615038 ∙ HGNC:26560 ∙ Uniprot:Q96M63 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 20 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 20 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 20	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	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Gastrointestinal; Pulmonary	23261302; 23261303

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODAD1 gene.

• Primary ciliary dyskinesia (356 variants)
• not provided (75 variants)
• not specified (40 variants)
• Inborn genetic diseases (28 variants)
• Primary ciliary dyskinesia 20 (24 variants)
• ODAD1-related condition (2 variants)
• Fraser syndrome 3 (1 variants)
• Kartagener syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODAD1 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				89	8	97
missense	1		168	20	11	200
nonsense	3	2				5
start loss						0
frameshift	6	2	4			12
inframe indel			8	1		9
splice donor/acceptor (+/-2bp)	4					4
splice region		2	5	9	4	20
non coding				27	18	45
Total	14	4	180	137	37

Highest pathogenic variant AF is 0.000204

Variants in ODAD1

This is a list of pathogenic ClinVar variants found in the ODAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48296734-C-T			Benign (Mar 25, 2019)
19-48296961-T-C		not specified	Benign (Nov 10, 2018)
19-48296979-G-A		Primary ciliary dyskinesia	Likely benign (Mar 25, 2022)
19-48296979-G-T			Likely benign (Aug 16, 2018)
19-48296983-C-T		Primary ciliary dyskinesia	Likely benign (Dec 19, 2023)
19-48296984-G-A		Primary ciliary dyskinesia	Uncertain significance (Jan 23, 2024)
19-48296995-C-G		Primary ciliary dyskinesia	Uncertain significance (Nov 18, 2023)
19-48296998-GTGG-TGT		Primary ciliary dyskinesia	Uncertain significance (Feb 22, 2018)
19-48297009-C-T		Primary ciliary dyskinesia	Likely benign (Nov 14, 2022)
19-48297009-CGGGCCAGTGCTGGAGGCA-C		Primary ciliary dyskinesia	Uncertain significance (Aug 13, 2021)
19-48297010-G-A		Primary ciliary dyskinesia	Uncertain significance (Jul 27, 2022)
19-48297015-A-AGTGCTGGAGGCAGGGCCG		Primary ciliary dyskinesia	Uncertain significance (Aug 09, 2022)
19-48297030-G-A		not specified • Primary ciliary dyskinesia	Likely benign (Feb 04, 2016)
19-48297033-G-A		Primary ciliary dyskinesia	Likely benign (Nov 22, 2022)
19-48297044-C-T		Primary ciliary dyskinesia	Conflicting classifications of pathogenicity (Nov 25, 2023)
19-48297053-T-C		Primary ciliary dyskinesia	Uncertain significance (Jul 21, 2023)
19-48297053-T-TGCTGGACCCGAGGCCTCC		Primary ciliary dyskinesia	Uncertain significance (Jun 27, 2022)
19-48297056-T-C		Primary ciliary dyskinesia	Uncertain significance (May 06, 2022)
19-48297060-C-T		Primary ciliary dyskinesia	Likely benign (Jun 01, 2022)
19-48297062-C-T		Primary ciliary dyskinesia	Uncertain significance (Aug 22, 2022)
19-48297063-G-A		Primary ciliary dyskinesia	Likely benign (Feb 02, 2023)
19-48297065-GGCCTCCGCTCGAATCAGACGCTGT-G		Primary ciliary dyskinesia	Uncertain significance (Mar 08, 2023)
19-48297071-C-T		Primary ciliary dyskinesia	Uncertain significance (Dec 17, 2020)
19-48297072-G-A		Primary ciliary dyskinesia	Likely benign (Jul 14, 2023)
19-48297072-G-T		Primary ciliary dyskinesia	Uncertain significance (Mar 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODAD1	protein_coding	protein_coding	ENST00000315396	13	25438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.63e-9	0.877	125715	0	27	125742	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.480	406	434	0.935	0.0000288	4381
Missense in Polyphen		119	144.17	0.8254		1559
Synonymous	1.18	169	190	0.891	0.0000131	1317
Loss of Function	1.71	17	26.5	0.641	0.00000122	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.000497	0.000496
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000733	0.0000703
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable component of the outer dynein arm complex required along the entire axoneme for tethering of outer dynein arms. {ECO:0000305|PubMed:23261302, ECO:0000305|PubMed:23261303}.
• Disease: DISEASE: Ciliary dyskinesia, primary, 20 (CILD20) [MIM:615067]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia. Patients may exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. Unlike other forms of CILD characterized by reduced fertility, patients with CILD20 do not appear to be infertile. {ECO:0000269|PubMed:23261302, ECO:0000269|PubMed:23261303}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.693
• rvis_EVS: 1.43
• rvis_percentile_EVS: 94.99

Haploinsufficiency Scores

• pHI: 0.0998
• hipred: N
• hipred_score: 0.172

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.205

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ccdc114

Gene ontology

• Biological process: cilium movement;outer dynein arm assembly
• Cellular component: cilium;axoneme;outer dynein arm
• Molecular function: protein binding