DNAH9

dynein axonemal heavy chain 9, the group of Dyneins, axonemal outer arm complex subunits

Basic information

Region (hg38): 17:11598470-11969748

Previous symbols: [ "DNAH17L" ]

Links

ENSG00000007174 ∙ NCBI:1770 ∙ OMIM:603330 ∙ HGNC:2953 ∙ Uniprot:Q9NYC9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• ciliary dyskinesia, primary, 40 (Strong), mode of inheritance: AR
• ciliary dyskinesia, primary, 40 (Moderate), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• situs inversus (Supportive), mode of inheritance: AD
• schizophrenia (Limited), mode of inheritance: AD
• ciliary dyskinesia, primary, 40 (Strong), mode of inheritance: AR
• ciliary dyskinesia, primary, 40 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 40	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Pulmonary	Individuals have been described with a relatively mild respiratory phenotype, but awareness may allow early diagnosis and prompt management of infections and related respiratory sequelae; Individuals may require surgery or other interventions related to congenital cardiac malformations	Allergy/Immunology/Infectious; Cardiovascular; Gastrointestinal; Pulmonary	30471717; 30471718

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAH9 gene.

• not provided (61 variants)
• DNAH9-related disorder (5 variants)
• Ciliary dyskinesia, primary, 40 (4 variants)
• Congenital heart disease (2 variants)
• Abnormal cardiovascular system morphology (1 variants)
• Non-immune hydrops fetalis (1 variants)
• Hydrocephalus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAH9 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			3	415	49	467
missense		1	786	35	45	867
nonsense	32	9	2			43
start loss			2			2
frameshift	27	9	2		1	39
inframe indel			8		1	9
splice donor/acceptor (+/-2bp)	4	27		1		32
splice region			25	55	2	82
non coding			7	180	141	328
Total	63	46	810	631	237

Highest pathogenic variant AF is 0.000309

Variants in DNAH9

This is a list of pathogenic ClinVar variants found in the DNAH9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-11598497-C-T		DNAH9-related disorder	Benign (Jun 18, 2019)
17-11598500-TGCGGCTCGCGGAGGAGCGGGCCGCGCTC-T			Pathogenic (Jun 17, 2023)
17-11598501-G-A			Uncertain significance (Sep 17, 2021)
17-11598503-G-T			Uncertain significance (Mar 05, 2024)
17-11598503-GGCTCGCGGAGGAGCGGGCCGC-G			Uncertain significance (Aug 23, 2022)
17-11598504-G-T			Likely benign (Aug 08, 2024)
17-11598505-C-G			Uncertain significance (Sep 06, 2023)
17-11598505-C-T			Uncertain significance (Nov 29, 2022)
17-11598507-C-A			Likely benign (Dec 23, 2024)
17-11598510-G-A			Likely benign (Jan 20, 2025)
17-11598513-G-A			Likely benign (Jul 26, 2022)
17-11598517-CGGGCCGCGCTCGCGGCGGAGAA-AACGCGGATGGGGAACCCGGCGCCGAC			Pathogenic (May 19, 2022)
17-11598522-C-G			Likely benign (May 27, 2022)
17-11598522-C-T			Likely benign (Jan 06, 2025)
17-11598525-G-T		DNAH9-related disorder	Likely benign (Apr 26, 2021)
17-11598528-C-T			Likely benign (Nov 04, 2023)
17-11598537-G-C		Inborn genetic diseases • Ciliary dyskinesia, primary, 40	Uncertain significance (Nov 19, 2022)
17-11598536-A-AGAACGCGGATGGGGAACCCGGCGCC			Pathogenic (Nov 07, 2024)
17-11598540-C-G		Inborn genetic diseases • DNAH9-related disorder	Conflicting classifications of pathogenicity (Jan 07, 2025)
17-11598539-A-ACGCGGATGGGGAACCCGGCGCCGAC		DNAH9-related disorder	Benign (Feb 03, 2025)
17-11598543-G-A			Likely benign (Mar 28, 2024)
17-11598554-C-G		Inborn genetic diseases	Uncertain significance (May 12, 2024)
17-11598558-C-A			Likely benign (Jun 19, 2024)
17-11598558-C-T			Likely benign (Mar 30, 2024)
17-11598559-G-T		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAH9	protein_coding	protein_coding	ENST00000262442	69	371318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-60	1.00	125231	0	517	125748	0.00206

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0429	2436	2.43e+3	1.00	0.000139	29535
Missense in Polyphen		660	714.46	0.92377		8620
Synonymous	0.640	920	945	0.974	0.0000555	8660
Loss of Function	5.03	130	208	0.624	0.0000106	2429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00421	0.00421
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.00398	0.00398
Finnish	0.00153	0.00153
European (Non-Finnish)	0.00194	0.00192
Middle Eastern	0.00398	0.00398
South Asian	0.00232	0.00232
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP.
• Pathway: Huntington,s disease - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.964
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.06

Haploinsufficiency Scores

• pHI: 0.210
• hipred: Y
• hipred_score: 0.593
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.544

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnah9

Gene ontology

• Biological process: microtubule-based movement;cell projection organization
• Cellular component: microtubule;axoneme;dynein complex;9+2 motile cilium;distal portion of axoneme
• Molecular function: ATP binding;ATP-dependent microtubule motor activity, minus-end-directed;dynein light chain binding;dynein intermediate chain binding;dynein light intermediate chain binding