DNAI2

dynein axonemal intermediate chain 2, the group of WD repeat domain containing|Dyneins, axonemal outer arm complex subunits

Basic information

Region (hg38): 17:74274233-74314884

Links

ENSG00000171595 ∙ NCBI:64446 ∙ OMIM:605483 ∙ HGNC:18744 ∙ Uniprot:Q9GZS0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia 9 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 9 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 9 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 9	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 may require surgery or other interventions related to congenital cardiac malformations	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Genitourinary; Pulmonary	18950741; 20301301; 23261302

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAI2 gene.

• Primary ciliary dyskinesia (595 variants)
• Primary ciliary dyskinesia 9 (110 variants)
• not provided (86 variants)
• not specified (43 variants)
• Inborn genetic diseases (16 variants)
• DNAI2-related condition (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAI2 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	233	6	241
missense	1	1	142	9	4	157
nonsense	21	3				24
start loss						0
frameshift	27	6				33
inframe indel			6			6
splice donor/acceptor (+/-2bp)	2	12	1			15
splice region	1		11	38	2	52
non coding			13	72	37	122
Total	51	22	164	314	47

Highest pathogenic variant AF is 0.0000788

Variants in DNAI2

This is a list of pathogenic ClinVar variants found in the DNAI2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74274284-GAGCCGCGACC-G		Primary ciliary dyskinesia	Benign (Jun 14, 2016)
17-74274303-A-G		Primary ciliary dyskinesia 9	Benign (Jan 12, 2018)
17-74274335-G-A		Primary ciliary dyskinesia 9	Uncertain significance (Jan 22, 2018)
17-74274336-C-A		Primary ciliary dyskinesia	Uncertain significance (Jun 14, 2016)
17-74274336-C-T		Primary ciliary dyskinesia 9	Uncertain significance (Jan 12, 2018)
17-74274340-C-A		Primary ciliary dyskinesia 9	Uncertain significance (Jan 13, 2018)
17-74281550-G-A			Benign (Nov 11, 2018)
17-74281606-G-C			Likely benign (May 27, 2021)
17-74281740-A-G		Primary ciliary dyskinesia 9	Benign (Jul 10, 2021)
17-74281811-C-T		DNAI2-related disorder	Likely benign (Oct 28, 2019)
17-74281814-C-T		Primary ciliary dyskinesia 9	Uncertain significance (Jan 12, 2018)
17-74281826-T-C		Primary ciliary dyskinesia	Likely benign (Jul 08, 2023)
17-74281828-T-C		Primary ciliary dyskinesia	Uncertain significance (Aug 27, 2021)
17-74281829-G-T		Primary ciliary dyskinesia	Likely benign (Jun 09, 2022)
17-74281832-C-A		Primary ciliary dyskinesia	Pathogenic (Aug 30, 2023)
17-74281832-C-T		Primary ciliary dyskinesia	Likely benign (May 17, 2021)
17-74281835-G-A		Primary ciliary dyskinesia	Likely benign (Nov 06, 2023)
17-74281838-C-G		Primary ciliary dyskinesia	Pathogenic (Jun 04, 2023)
17-74281838-C-T		Primary ciliary dyskinesia	Likely benign (Dec 01, 2023)
17-74281844-G-A		Primary ciliary dyskinesia	Likely benign (Jan 27, 2021)
17-74281847-G-A		Primary ciliary dyskinesia	Likely benign (Jan 26, 2023)
17-74281849-G-A		Primary ciliary dyskinesia	Uncertain significance (Nov 04, 2021)
17-74281850-C-A		Primary ciliary dyskinesia	Likely benign (Sep 27, 2023)
17-74281850-C-T		Primary ciliary dyskinesia	Likely benign (Jun 09, 2023)
17-74281853-C-T		Primary ciliary dyskinesia	Likely benign (Sep 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAI2	protein_coding	protein_coding	ENST00000446837	12	40638

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.53e-13	0.689	125626	0	122	125748	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	336	359	0.937	0.0000231	4005
Missense in Polyphen		60	66.299	0.90499		674
Synonymous	-0.371	156	150	1.04	0.0000116	1110
Loss of Function	1.64	24	34.4	0.698	0.00000195	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00100	0.000999
Ashkenazi Jewish	0.00337	0.00338
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000310	0.000308
Middle Eastern	0.000326	0.000326
South Asian	0.000817	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the dynein complex of respiratory cilia.
• Pathway: Huntington,s disease - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.619
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.12

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.238
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.403

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnaic2
• Phenotype: growth/size/body region phenotype; cellular phenotype; respiratory system phenotype

Gene ontology

• Biological process: cilium movement;microtubule-based movement;determination of left/right symmetry;outer dynein arm assembly;cilium assembly
• Cellular component: axonemal dynein complex;microtubule;axoneme;external side of plasma membrane;dynein complex;sperm flagellum;outer dynein arm
• Molecular function: microtubule motor activity;protein binding;ATP-dependent microtubule motor activity, plus-end-directed;dynein light chain binding;dynein heavy chain binding