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_specified (663 variants)
not_provided (220 variants)
DNHD1-related_disorder (103 variants)
Spermatogenic_failure_65 (32 variants)
DNHD1-related_Neurodevelopmental_Disorder (2 variants)
Male_infertility_with_spermatogenesis_disorder (2 variants)
DNHD1-related_Intellectual_Disability (2 variants)
See_cases (2 variants)
Essential_tremor (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. These statistics are base on transcript: NM_000144666.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	71 clinvar	18 clinvar	95
missense	1 clinvar	2 clinvar	654 clinvar	89 clinvar	17 clinvar	763
nonsense	10 clinvar	11 clinvar	3 clinvar	3 clinvar		27
start loss						0
frameshift	10 clinvar	8 clinvar	6 clinvar	1 clinvar		25
splice donor/acceptor (+/-2bp)		8 clinvar	5 clinvar	2 clinvar		15
Total	21	29	674	166	35

Highest pathogenic variant AF is 0.0012289572

Loading clinvar variants...

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
Phenotype

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