DNHD1

dynein heavy chain domain 1

Basic information

Region (hg38): 11:6497260-6593758

Previous symbols: [ "DHCD1", "C11orf47", "DNHD1L", "CCDC35" ]

Links

ENSG00000179532 ∙ NCBI:144132 ∙ OMIM:617277 ∙ HGNC:26532 ∙ Uniprot:Q96M86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 65 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 65	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	34932939

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNHD1 gene.

• not provided (21 variants)
• Spermatogenic failure 65 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNHD1 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	68	25	94
missense		2	296	61	42	401
nonsense	11	6	1	3		21
start loss						0
frameshift	10	2	1	1		14
inframe indel					1	1
splice donor/acceptor (+/-2bp)		4	1	2		7
splice region				4	3	7
non coding		1		3	1	5
Total	21	15	300	138	69

Highest pathogenic variant AF is 0.000466

Variants in DNHD1

This is a list of pathogenic ClinVar variants found in the DNHD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6498224-G-A		DNHD1-related disorder	Benign/Likely benign (Mar 01, 2024)
11-6498279-T-G		not specified	Uncertain significance (Dec 19, 2023)
11-6498282-T-A		not specified	Uncertain significance (Mar 07, 2024)
11-6498285-C-A		DNHD1-related disorder	Likely benign (Dec 31, 2019)
11-6498295-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-6498300-T-C			Likely benign (Nov 01, 2024)
11-6498310-A-G		not specified	Uncertain significance (Oct 10, 2023)
11-6498319-C-T		not specified	Uncertain significance (Dec 19, 2022)
11-6498331-A-G		DNHD1-related disorder	Likely benign (Oct 01, 2023)
11-6498412-G-A		DNHD1-related disorder	Benign (Oct 21, 2019)
11-6498463-A-G			Uncertain significance (May 01, 2024)
11-6498498-C-A		not specified	Uncertain significance (Sep 17, 2021)
11-6498499-G-A		not specified	Uncertain significance (Apr 19, 2023)
11-6498516-C-T		not specified	Uncertain significance (Jan 18, 2022)
11-6498523-A-T		not specified	Uncertain significance (Feb 27, 2024)
11-6498588-G-C		not specified	Uncertain significance (Aug 20, 2024)
11-6498597-G-A		not specified	Uncertain significance (Dec 06, 2024)
11-6498603-A-G		not specified	Uncertain significance (Apr 27, 2023)
11-6498645-G-A		not specified	Uncertain significance (Oct 06, 2023)
11-6498653-T-G		not specified	Uncertain significance (May 20, 2024)
11-6498656-T-G			Likely benign (Sep 07, 2018)
11-6498712-C-T		not specified	Uncertain significance (Mar 15, 2024)
11-6498732-AGCAG-A		Spermatogenic failure 65	Pathogenic (Jun 28, 2022)
11-6498741-C-G		not specified	Uncertain significance (Jul 09, 2024)
11-6498745-T-G		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNHD1	protein_coding	protein_coding	ENST00000254579	41	96499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-72	0.464	125052	2	694	125748	0.00277

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.48	2080	2.58e+3	0.807	0.000150	30563
Missense in Polyphen		555	777.56	0.71377		9900
Synonymous	4.38	879	1.06e+3	0.829	0.0000580	9981
Loss of Function	3.97	147	209	0.703	0.0000121	2132

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0170	0.0164
Ashkenazi Jewish	0.00	0.00
East Asian	0.00312	0.00305
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00200	0.00195
Middle Eastern	0.00312	0.00305
South Asian	0.000949	0.000948
Other	0.00265	0.00261

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.953
• rvis_EVS: 6.68
• rvis_percentile_EVS: 99.88

Haploinsufficiency Scores

• pHI: 0.0832
• hipred: N
• hipred_score: 0.173
• ghis: 0.397

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnhd1

Gene ontology

• Biological process: microtubule-based movement
• Cellular component: dynein complex;extracellular exosome
• 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