ZMYND10

zinc finger MYND-type containing 10, the group of Axonemal dynein assembly factors|Zinc fingers MYND-type

Basic information

Region (hg38): 3:50341109-50345732

Links

ENSG00000004838 ∙ NCBI:51364 ∙ OMIM:607070 ∙ HGNC:19412 ∙ Uniprot:O75800 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary ciliary dyskinesia 22 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 22 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 22 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia 22 (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Supportive), mode of inheritance: AD
• primary ciliary dyskinesia 22 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Ciliary dyskinesia, primary, 22	AR	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Pulmonary	Pulmonary and audiologic surveillance may be beneficial to assess respiratory and hearing 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, though measures including lobectomy or lung transplantation may be necessary; The condition can involve congenital cardiac anomalies, and awareness may allow early management	Allergy/Immunology/Infectious; Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal	20301301; 23891469; 23891471
The condition can involve multiple anomalies, and individuals may require surgery or other interventions related to findings such as congenital cardiac malformations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYND10 gene.

• Primary ciliary dyskinesia (155 variants)
• not provided (17 variants)
• Primary ciliary dyskinesia 22 (14 variants)
• Inborn genetic diseases (14 variants)
• ZMYND10-related condition (2 variants)
• Kartagener syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND10 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				30	1	31
missense	3		76	10		89
nonsense	4	2	1			7
start loss						0
frameshift	3	2				5
inframe indel						0
splice donor/acceptor (+/-2bp)		4	1			5
splice region			3	3	2	8
non coding	1		3	18	6	28
Total	11	8	81	58	7

Highest pathogenic variant AF is 0.000197

Variants in ZMYND10

This is a list of pathogenic ClinVar variants found in the ZMYND10 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50341197-A-G			Benign (Nov 13, 2018)
3-50341276-C-A			Likely benign (Mar 03, 2019)
3-50341416-G-A		Primary ciliary dyskinesia	Likely benign (Sep 13, 2018)
3-50341442-C-T		Primary ciliary dyskinesia	Uncertain significance (Sep 26, 2023)
3-50341452-T-C		Primary ciliary dyskinesia	Likely benign (Jul 25, 2018)
3-50341463-C-T		Primary ciliary dyskinesia	Uncertain significance (Nov 21, 2018)
3-50341474-A-G		Inborn genetic diseases	Uncertain significance (May 22, 2023)
3-50341480-C-CT		Primary ciliary dyskinesia	Uncertain significance (Jun 12, 2017)
3-50341486-C-A		Primary ciliary dyskinesia 22	Likely pathogenic (Sep 25, 2023)
3-50341515-A-G			Benign (Nov 13, 2018)
3-50341556-G-T		Primary ciliary dyskinesia	Likely benign (Dec 04, 2022)
3-50341583-T-C		Primary ciliary dyskinesia	Uncertain significance (Sep 27, 2019)
3-50341601-C-G		Primary ciliary dyskinesia	Uncertain significance (May 07, 2022)
3-50341610-C-T		Primary ciliary dyskinesia	Uncertain significance (Sep 24, 2018)
3-50341624-T-C		Primary ciliary dyskinesia	Likely benign (Aug 10, 2023)
3-50341643-C-T		Primary ciliary dyskinesia	Uncertain significance (Aug 26, 2021)
3-50341644-G-A		Primary ciliary dyskinesia	Uncertain significance (Jun 28, 2022)
3-50341644-G-C		Primary ciliary dyskinesia	Uncertain significance (Aug 06, 2022)
3-50341649-C-T		Primary ciliary dyskinesia	Uncertain significance (Jul 27, 2022)
3-50341650-G-A		Primary ciliary dyskinesia • Primary ciliary dyskinesia 22	Uncertain significance (Mar 19, 2022)
3-50341653-C-T		Primary ciliary dyskinesia	Uncertain significance (Jul 16, 2020)
3-50341658-G-A		Primary ciliary dyskinesia	Uncertain significance (Aug 24, 2021)
3-50341666-C-T		Primary ciliary dyskinesia	Likely benign (Nov 18, 2023)
3-50341681-C-T		Primary ciliary dyskinesia	Likely benign (Oct 19, 2020)
3-50341684-G-A		Primary ciliary dyskinesia	Likely benign (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND10	protein_coding	protein_coding	ENST00000231749	12	5743

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.30e-7	0.976	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.932	208	249	0.834	0.0000137	2841
Missense in Polyphen		39	51.692	0.75447		599
Synonymous	1.58	82	102	0.802	0.00000518	867
Loss of Function	2.12	15	26.9	0.558	0.00000133	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.000381	0.000381
South Asian	0.0000327	0.0000327
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in axonemal structure organization and motility (PubMed:23891469, PubMed:23891471). Involved in axonemal pre-assembly of inner and outer dynein arms (IDA and ODA, respectively) for proper axoneme building for cilia motility (By similarity). May act by indirectly regulating transcription of dynein proteins (By similarity). {ECO:0000250|UniProtKB:Q99ML0, ECO:0000269|PubMed:23891469, ECO:0000269|PubMed:23891471}.
• Disease: DISEASE: Ciliary dyskinesia, primary, 22 (CILD22) [MIM:615444]: 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. Patients may 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. {ECO:0000269|PubMed:23891469, ECO:0000269|PubMed:23891471, ECO:0000269|PubMed:25186273, ECO:0000269|PubMed:29601588}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.226

Intolerance Scores

• loftool: 0.443
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.251
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.721

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Zmynd10
• Phenotype: immune system 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); 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); respiratory system phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: zmynd10
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: outer dynein arm assembly;inner dynein arm assembly;motile cilium assembly;positive regulation of motile cilium assembly
• Cellular component: cytoplasm;apical plasma membrane;centriolar satellite
• Molecular function: protein binding;metal ion binding