DNAH3

dynein axonemal heavy chain 3, the group of Dyneins, axonemal inner arm I1/f complex subunits

Basic information

Region (hg38): 16:20933110-21159441

Links

ENSG00000158486 ∙ NCBI:55567 ∙ OMIM:603334 ∙ HGNC:2949 ∙ Uniprot:Q8TD57 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAH3 gene.

• Inborn genetic diseases (180 variants)
• not provided (41 variants)
• not specified (8 variants)
• Spermatogenic failure 18 (6 variants)
• Intellectual disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAH3 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				15	11	26
missense	1	2	172	18	5	198
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding						0
Total	1	3	172	33	16

Highest pathogenic variant AF is 0.0000854

Variants in DNAH3

This is a list of pathogenic ClinVar variants found in the DNAH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20933162-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-20933198-A-G		not specified	Uncertain significance (Feb 21, 2024)
16-20933219-T-C		not specified	Uncertain significance (Jan 22, 2024)
16-20933226-C-G		not specified	Uncertain significance (Jan 24, 2024)
16-20933237-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-20933391-G-A			Benign (Dec 31, 2019)
16-20933462-C-G		not specified	Uncertain significance (Aug 02, 2021)
16-20933475-G-C		not specified	Uncertain significance (Jun 22, 2023)
16-20935342-C-T			Benign (Sep 01, 2017)
16-20935380-T-C		Intellectual disability	Uncertain significance (Oct 16, 2020)
16-20935391-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-20935410-C-T		not specified	Uncertain significance (Oct 03, 2022)
16-20936782-G-A		not specified	Uncertain significance (Jan 10, 2022)
16-20936837-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-20936845-T-C		not specified	Uncertain significance (Mar 06, 2023)
16-20941452-T-C		not specified	Uncertain significance (Jan 06, 2023)
16-20941474-T-A		not specified	Uncertain significance (Jul 14, 2021)
16-20941519-C-A		not specified	Uncertain significance (Nov 09, 2021)
16-20944531-G-C		not specified	Uncertain significance (Aug 08, 2022)
16-20948527-C-T		not specified	Uncertain significance (Dec 14, 2022)
16-20948608-C-T		not specified	Uncertain significance (Dec 02, 2021)
16-20952443-G-C			Benign (Dec 31, 2019)
16-20952510-C-T			Benign (Jul 20, 2018)
16-20952513-A-C		not specified	Uncertain significance (Jun 22, 2021)
16-20952517-C-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAH3	protein_coding	protein_coding	ENST00000261383	62	226330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.54e-64	0.859	124711	1	1036	125748	0.00413

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0299	2256	2.26e+3	0.998	0.000129	27273
Missense in Polyphen		846	869.11	0.97341		10465
Synonymous	-2.13	970	889	1.09	0.0000555	7742
Loss of Function	3.96	132	191	0.691	0.00000985	2291

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00758	0.00728
Ashkenazi Jewish	0.000796	0.000794
East Asian	0.00333	0.00332
Finnish	0.0124	0.0124
European (Non-Finnish)	0.00386	0.00379
Middle Eastern	0.00333	0.00332
South Asian	0.00269	0.00262
Other	0.00326	0.00326

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. Involved in sperm motility; implicated in sperm flagellar assembly (By similarity). {ECO:0000250}.
• Pathway: Huntington,s disease - Homo sapiens (human);lissencephaly gene (lis1) in neuronal migration and development (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.980
• rvis_EVS: -1.47
• rvis_percentile_EVS: 3.73

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.492
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.200

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnah3

Gene ontology

• Biological process: cilium movement;microtubule-based movement;cilium-dependent cell motility
• Cellular component: axonemal dynein complex;microtubule;dynein complex
• Molecular function: microtubule motor activity;ATP binding;ATP-dependent microtubule motor activity, minus-end-directed;dynein light chain binding;dynein intermediate chain binding;dynein light intermediate chain binding