DNAI1

dynein axonemal intermediate chain 1, the group of Dyneins, axonemal outer arm complex subunits|WD repeat domain containing

Basic information

Region (hg38): 9:34457414-34520988

Links

ENSG00000122735 ∙ NCBI:27019 ∙ OMIM:604366 ∙ HGNC:2954 ∙ Uniprot:Q9UI46 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia 1 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 1 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 1 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 1	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; Genitourinary; Pulmonary	10577904; 11231901; 11893720; 16858015; 18434704; 19300264; 20301301; 21143860; 22416021; 22499950

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAI1 gene.

• Primary ciliary dyskinesia (77 variants)
• Kartagener syndrome (5 variants)
• not provided (1 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAI1 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	261		262
missense	2	6	158	15		181
nonsense	25	5				30
start loss	2					2
frameshift	40	2				42
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)	8	32				40
splice region	1	1	10	54	3	69
non coding			8	171	22	201
Total	77	45	169	448	22

Highest pathogenic variant AF is 0.000440

Variants in DNAI1

This is a list of pathogenic ClinVar variants found in the DNAI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34458826-G-A		Kartagener syndrome	Uncertain significance (Jan 12, 2018)
9-34458828-G-C		Primary ciliary dyskinesia	Likely benign (Nov 12, 2018)
9-34458836-T-A		Primary ciliary dyskinesia	Uncertain significance (Jun 14, 2016)
9-34458861-C-T		Kartagener syndrome	Uncertain significance (Jan 12, 2018)
9-34458890-T-C		Kartagener syndrome	Likely benign (Jan 12, 2018)
9-34458923-G-C		Kartagener syndrome	Uncertain significance (Jan 13, 2018)
9-34458965-T-C		Primary ciliary dyskinesia	Uncertain significance (Jun 14, 2016)
9-34459001-TTGAGA-T		Primary ciliary dyskinesia	Pathogenic (Aug 22, 2022)
9-34459006-A-G		Primary ciliary dyskinesia	Pathogenic (Nov 09, 2023)
9-34459012-C-T		Primary ciliary dyskinesia	Uncertain significance (Jul 23, 2020)
9-34459020-T-C		Primary ciliary dyskinesia	Likely benign (Aug 02, 2023)
9-34459023-G-A		Primary ciliary dyskinesia	Likely benign (Jul 16, 2023)
9-34459027-G-C		Primary ciliary dyskinesia • Kartagener syndrome	Uncertain significance (Aug 20, 2021)
9-34459027-G-T		not specified • Primary ciliary dyskinesia	Benign/Likely benign (Feb 01, 2024)
9-34459030-C-G		Primary ciliary dyskinesia	Uncertain significance (May 06, 2019)
9-34459032-C-T		Primary ciliary dyskinesia	Likely benign (Dec 02, 2021)
9-34459045-C-T		Primary ciliary dyskinesia	Conflicting classifications of pathogenicity (Jan 28, 2024)
9-34459048-A-T		Primary ciliary dyskinesia	Pathogenic (Aug 06, 2022)
9-34459050-G-T		Primary ciliary dyskinesia	Uncertain significance (Apr 11, 2023)
9-34459052-A-G		not specified • Primary ciliary dyskinesia • DNAI1-related disorder	Conflicting classifications of pathogenicity (Jun 06, 2024)
9-34459053-G-T		Primary ciliary dyskinesia	Uncertain significance (Aug 10, 2022)
9-34459054-G-C		Primary ciliary dyskinesia	Likely pathogenic (Apr 06, 2021)
9-34459054-G-T		Primary ciliary dyskinesia	Likely pathogenic (Apr 13, 2022)
9-34459054-G-GT		Kartagener syndrome • Primary ciliary dyskinesia • Inborn genetic diseases • DNAI1-related disorder	Pathogenic (Jan 27, 2024)
9-34459056-A-G		Primary ciliary dyskinesia	Uncertain significance (Mar 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAI1	protein_coding	protein_coding	ENST00000242317	20	63571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-8	0.999	125496	2	250	125748	0.00100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.292	382	366	1.04	0.0000205	4633
Missense in Polyphen		78	84.621	0.92176		1039
Synonymous	-1.64	170	145	1.17	0.00000901	1273
Loss of Function	2.91	19	38.4	0.494	0.00000179	503

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.00248	0.00238
East Asian	0.0000544	0.0000544
Finnish	0.000416	0.000416
European (Non-Finnish)	0.00138	0.00137
Middle Eastern	0.0000544	0.0000544
South Asian	0.000327	0.000327
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the dynein complex of respiratory cilia.
• Disease: DISEASE: Ciliary dyskinesia, primary, 1 (CILD1) [MIM:244400]: 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; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients 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. {ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Kartagener syndrome (KTGS) [MIM:244400]: An autosomal recessive disorder characterized by the association of primary ciliary dyskinesia with situs inversus. Clinical features include recurrent respiratory infections, bronchiectasis, infertility, and lateral transposition of the viscera of the thorax and abdomen. The situs inversus is most often total, although it can be partial in some cases (isolated dextrocardia or isolated transposition of abdominal viscera). {ECO:0000269|PubMed:11231901}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Huntington,s disease - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.603
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.23

Haploinsufficiency Scores

• pHI: 0.314
• hipred: N
• hipred_score: 0.443
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnaic1
• Phenotype: cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; respiratory system phenotype; immune system phenotype; skeleton 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); 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)

Gene ontology

• Biological process: cilium movement;microtubule-based movement;determination of left/right symmetry;flagellated sperm motility;outer dynein arm assembly
• Cellular component: cytoskeleton;microtubule;cilium;dynein complex;outer dynein arm
• Molecular function: motor activity;protein binding;ATP-dependent microtubule motor activity, plus-end-directed;dynein light chain binding;dynein heavy chain binding