HYDIN

HYDIN axonemal central pair apparatus protein, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 16:70802084-71230722

Links

ENSG00000157423 ∙ NCBI:54768 ∙ OMIM:610812 ∙ HGNC:19368 ∙ Uniprot:Q4G0P3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia 5 (Definitive), mode of inheritance: AR
• primary ciliary dyskinesia 5 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 5 (Moderate), mode of inheritance: AR
• primary ciliary dyskinesia 5 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 5 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 5	AR	Allergy/Immunology/Infectious; Pulmonary	Pulmonary surveillance may be beneficial to assess respiratory 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	Allergy/Immunology/Infectious; Gastrointestinal; Pulmonary	14985390; 23022101; 23849777

ClinVar

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

• Primary ciliary dyskinesia 5 (9 variants)
• Primary ciliary dyskinesia (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HYDIN 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	74	3	79
missense		1	184	39	5	229
nonsense	6	10	1			17
start loss						0
frameshift	4	13	3			20
inframe indel		1	3		1	5
splice donor/acceptor (+/-2bp)	1	4	1			6
splice region			4	7		11
non coding			3	2	6	11
Total	11	29	197	115	15

Highest pathogenic variant AF is 0.000269

Variants in HYDIN

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

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

Position	Type	Phenotype	Significance	ClinVar
16-70807737-C-T			Uncertain significance (Dec 01, 2023)
16-70807754-G-A		HYDIN-related disorder	Likely benign (Mar 10, 2023)
16-70807800-A-G		HYDIN-related disorder	Likely benign (Apr 11, 2019)
16-70807844-G-A		HYDIN-related disorder	Likely benign (May 28, 2019)
16-70807854-G-A		Primary ciliary dyskinesia 5	Uncertain significance (Feb 13, 2018)
16-70807898-GGGGATGATATA-TATATCATC		Primary ciliary dyskinesia 5	Likely pathogenic (Mar 06, 2024)
16-70808014-C-T		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
16-70808060-G-A		HYDIN-related disorder	Likely benign (May 24, 2019)
16-70808065-G-GA			Likely benign (Mar 01, 2023)
16-70809809-G-A		Primary ciliary dyskinesia 5	Conflicting classifications of pathogenicity (Feb 01, 2024)
16-70809924-G-C			Likely pathogenic (Jul 01, 2019)
16-70818337-C-T		Primary ciliary dyskinesia 5	Uncertain significance (Nov 15, 2018)
16-70818377-G-C			Likely benign (Sep 01, 2023)
16-70818381-G-A			Likely benign (Apr 01, 2022)
16-70818387-G-A			Likely benign (Oct 01, 2022)
16-70818496-A-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
16-70828356-T-C		Inborn genetic diseases	Uncertain significance (Aug 12, 2021)
16-70828385-A-C		Primary ciliary dyskinesia 5	Likely pathogenic (Mar 06, 2024)
16-70829742-G-A			Uncertain significance (Feb 01, 2023)
16-70829792-C-T			Likely benign (Feb 01, 2023)
16-70829806-G-T			Uncertain significance (Nov 01, 2022)
16-70829903-T-C		not specified	Benign (May 04, 2022)
16-70832953-C-T			Likely benign (Sep 01, 2022)
16-70833037-AG-A		Primary ciliary dyskinesia 5	Pathogenic (Mar 06, 2024)
16-70833070-T-C		Primary ciliary dyskinesia 5	Uncertain significance (Mar 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HYDIN	protein_coding	protein_coding	ENST00000393567	85	423345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.27e-24	1.00	125524	0	224	125748	0.000891

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.810	1990	2.09e+3	0.950	0.000117	33454
Missense in Polyphen		709	809.39	0.87597		12630
Synonymous	-0.966	853	818	1.04	0.0000486	9768
Loss of Function	7.14	72	173	0.415	0.00000935	2805

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00121
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000177	0.000163
Finnish	0.00467	0.00463
European (Non-Finnish)	0.000687	0.000659
Middle Eastern	0.000177	0.000163
South Asian	0.000500	0.000490
Other	0.000517	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for ciliary motility. {ECO:0000250}.
• Disease: DISEASE: Ciliary dyskinesia, primary, 5 (CILD5) [MIM:608647]: An autosomal recessive form of primary dyskinesia, a disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. CILD5 is characterized by early onset of a progressive decline in lung function due to an inability to clear mucus and particles from the airways. Affected individuals have recurrent infections of the sinuses, ears, airways, and lungs. Sperm motility is also decreased. Individuals with CILD5 do not have situs inversus. {ECO:0000269|PubMed:23022101, ECO:0000269|PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Haploinsufficiency Scores

• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hydin
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; muscle phenotype

Gene ontology

• Biological process: epithelial cell development;cilium movement;ventricular system development;trachea development;axonemal central apparatus assembly
• Cellular component: axonemal central pair projection