ODAD2

outer dynein arm docking complex subunit 2, the group of Outer dynein arm docking complex subunits|Armadillo repeat containing

Basic information

Region (hg38): 10:27775186-27999079

Previous symbols: [ "ARMC4" ]

Links

ENSG00000169126 ∙ NCBI:55130 ∙ OMIM:615408 ∙ HGNC:25583 ∙ Uniprot:Q5T2S8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 23 (Definitive), mode of inheritance: AR
• primary ciliary dyskinesia 23 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 23 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 23	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; 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 may require surgery or other interventions related to congenital cardiac malformations	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Pulmonary	23849778; 24203976

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ODAD2 gene.

• Primary ciliary dyskinesia 23 (27 variants)
• not provided (4 variants)
• Primary ciliary dyskinesia (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ODAD2 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			1	111	5	117
missense		1	226	17	8	252
nonsense	13	2				15
start loss						0
frameshift	16	1				17
inframe indel						0
splice donor/acceptor (+/-2bp)	1	6				7
splice region			6	27	4	37
non coding			1	71	54	126
Total	30	10	228	199	67

Highest pathogenic variant AF is 0.0000789

Variants in ODAD2

This is a list of pathogenic ClinVar variants found in the ODAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-27812184-CTT-C			Benign (Nov 27, 2018)
10-27812382-T-C			Benign (Jan 16, 2019)
10-27812518-G-A		Primary ciliary dyskinesia 23	Likely benign (Dec 30, 2021)
10-27812526-C-A		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia	Benign (Jan 29, 2024)
10-27812526-C-T		Primary ciliary dyskinesia	Uncertain significance (Sep 29, 2022)
10-27812533-T-G		Primary ciliary dyskinesia 23	Likely benign (Jun 22, 2021)
10-27812534-G-C		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia	Uncertain significance (Jan 31, 2022)
10-27812537-G-A		Primary ciliary dyskinesia	Uncertain significance (Feb 20, 2022)
10-27812539-A-G		Primary ciliary dyskinesia	Likely benign (Jul 29, 2023)
10-27812548-C-A		Primary ciliary dyskinesia	Uncertain significance (May 17, 2023)
10-27812552-C-T		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia	Uncertain significance (Nov 25, 2023)
10-27812553-G-A		Primary ciliary dyskinesia	Uncertain significance (Mar 25, 2022)
10-27812561-G-A		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia • ODAD2-related disorder	Conflicting classifications of pathogenicity (Dec 28, 2023)
10-27812570-C-T			Uncertain significance (Jul 07, 2020)
10-27812578-A-G		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia	Likely benign (Jan 17, 2024)
10-27812591-T-A		Primary ciliary dyskinesia 23	Uncertain significance (May 28, 2022)
10-27812594-T-C		Primary ciliary dyskinesia	Uncertain significance (Nov 07, 2023)
10-27812603-G-T		Primary ciliary dyskinesia	Uncertain significance (Jun 12, 2022)
10-27812609-ACCATATC-A		Primary ciliary dyskinesia 23 • Primary ciliary dyskinesia	Conflicting classifications of pathogenicity (Nov 17, 2021)
10-27812617-C-T		Primary ciliary dyskinesia 23	Likely benign (Jun 13, 2023)
10-27812623-A-T		Primary ciliary dyskinesia 23	Likely benign (Oct 14, 2022)
10-27812643-GAGA-G		Primary ciliary dyskinesia 23	Likely benign (Apr 24, 2023)
10-27853365-T-TATAA		ODAD2-related disorder	Benign (Jul 30, 2019)
10-27853365-T-TATAAATAAATAAATAA		ODAD2-related disorder	Benign (Jun 20, 2019)
10-27853365-T-TATAAATAAATAA		ODAD2-related disorder	Benign (Aug 08, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ODAD2	protein_coding	protein_coding	ENST00000305242	19	223863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.90e-25	0.00253	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.511	526	560	0.939	0.0000304	6793
Missense in Polyphen		174	199.31	0.87299		2388
Synonymous	0.389	194	201	0.965	0.0000109	2005
Loss of Function	0.700	41	46.1	0.889	0.00000210	657

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00159	0.00156
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000660	0.000653
Finnish	0.0000933	0.0000924
European (Non-Finnish)	0.000674	0.000668
Middle Eastern	0.000660	0.000653
South Asian	0.000465	0.000457
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ciliary protein that may be involved in a late step of axonemal outer dynein arm assembly. {ECO:0000269|PubMed:23849778}.

Recessive Scores

• pRec: 0.0909

Intolerance Scores

• loftool: 0.380
• rvis_EVS: 1.12
• rvis_percentile_EVS: 92.09

Haploinsufficiency Scores

• pHI: 0.0769
• hipred: N
• hipred_score: 0.251

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.131

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Armc4
• Phenotype: growth/size/body region phenotype; muscle phenotype; immune system phenotype; cellular phenotype; respiratory system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: armc4
• Affected structure: heart looping
• Phenotype tag: abnormal
• Phenotype quality: process quality

Gene ontology

• Biological process: cilium movement;regulation of cilium beat frequency;determination of left/right symmetry;heart development;ventricular system development;outer dynein arm assembly
• Cellular component: axoneme;ciliary base