ZMYND10

Summary

ZMYND10 (zinc finger MYND-type containing 10, HGNC:19412) is a protein-coding gene on chromosome 3p21.31, encoding Zinc finger MYND domain-containing protein 10 (O75800). Plays a role in axonemal structure organization and motility.

This gene encodes a protein containing a MYND-type zinc finger domain that likely functions in assembly of the dynein motor. Mutations in this gene can cause primary ciliary dyskinesia. This gene is also considered a tumor suppressor gene and is often mutated, deleted, or hypermethylated and silenced in cancer cells. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 51364 — RefSeq curated summary.

At a glance

• Gene–disease (curated): primary ciliary dyskinesia 22 (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 6
• Clinical variants (ClinVar): 300 total — 20 pathogenic, 10 likely-pathogenic
• Phenotypes (HPO): 63
• MANE Select transcript: NM_015896

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19412
Approved symbol	ZMYND10
Name	zinc finger MYND-type containing 10
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	BLU, CILD22, DNAAF7
Ensembl gene	ENSG00000004838
Ensembl biotype	protein_coding
OMIM	607070
Entrez	51364

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 10 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000231749, ENST00000360165, ENST00000431869, ENST00000442887, ENST00000443080, ENST00000468182, ENST00000475688, ENST00000478269, ENST00000490675, ENST00000874784, ENST00000874785, ENST00000874786, ENST00000874787, ENST00000966238, ENST00000966239, ENST00000966240

RefSeq mRNA: 2 — MANE Select: NM_015896 NM_001308379, NM_015896

CCDS: CCDS2825, CCDS77747

Canonical transcript exons

ENST00000231749 — 12 exons

Exon	Start	End
ENSE00001598571	50342397	50342569
ENSE00001654103	50342015	50342140
ENSE00001806257	50343307	50343444
ENSE00001907585	50345488	50345732
ENSE00003476372	50341574	50341699
ENSE00003540543	50341810	50341931
ENSE00003542951	50343118	50343206
ENSE00003557022	50345124	50345232
ENSE00003609236	50343563	50343616
ENSE00003617096	50342918	50343018
ENSE00003627223	50343734	50343850
ENSE00003681381	50341112	50341485

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 99.32.

FANTOM5 (CAGE): breadth broad, TPM avg 1.1619 / max 388.8353, expressed in 323 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
42335	1.1116	293
202761	0.0412	11
42334	0.0091	3

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.32	gold quality
left testis	UBERON:0004533	98.96	gold quality
right testis	UBERON:0004534	98.76	gold quality
bronchial epithelial cell	CL:0002328	97.46	gold quality
epithelium of bronchus	UBERON:0002031	96.95	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.45	gold quality
bronchus	UBERON:0002185	95.68	gold quality
testis	UBERON:0000473	95.59	gold quality
adult organism	UBERON:0007023	93.83	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.71	gold quality
mucosa of paranasal sinus	UBERON:0005030	87.80	gold quality
right lung	UBERON:0002167	81.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.94	gold quality
nasal cavity epithelium	UBERON:0005384	80.90	gold quality
nucleus accumbens	UBERON:0001882	80.54	gold quality
granulocyte	CL:0000094	79.88	gold quality
caudate nucleus	UBERON:0001873	78.31	gold quality
left uterine tube	UBERON:0001303	78.10	gold quality
adenohypophysis	UBERON:0002196	77.87	gold quality
nasal cavity mucosa	UBERON:0001826	76.10	gold quality
pituitary gland	UBERON:0000007	75.45	gold quality
ventricular zone	UBERON:0003053	75.33	gold quality
hypothalamus	UBERON:0001898	75.17	gold quality
upper lobe of left lung	UBERON:0008952	74.49	gold quality
upper lobe of lung	UBERON:0008948	73.60	gold quality
amygdala	UBERON:0001876	72.70	gold quality
cerebellar hemisphere	UBERON:0002245	72.47	gold quality
putamen	UBERON:0001874	72.44	gold quality
cerebellar cortex	UBERON:0002129	72.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	72.25	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	924.05
E-MTAB-8221	yes	807.04
E-MTAB-10283	yes	769.49
E-CURD-114	yes	647.86
E-HCAD-1	yes	30.32
E-MTAB-10287	yes	26.90
E-GEOD-130148	yes	12.03
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting ZMYND10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-4664-5P	98.17	65.07	1020
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-4693-5P	97.35	67.02	1234
HSA-MIR-342-5P	97.25	64.10	817
HSA-MIR-212-5P	96.83	67.43	950
HSA-MIR-1293	96.16	64.69	916
HSA-MIR-3622B-5P	94.62	64.58	835

Literature-anchored findings (GeneRIF, showing 19)

• These data suggest a significant role for epigenetic inactivation of BLU in the pathogenesis of common human cancers and that methylation inactivation of BLU occurs independent of RASSF1A in SCLC and neuroblastoma tumours. (PMID:12629521)
• BLU may be one of the critical tumor suppressor genes on chromosome 3p21.3 involved in the development of nasopharyngeal carcinoma (PMID:12794757)
• BLU, a candidate tumor suppressor gene, located at the commonly deleted region 3p21.3, is an E2F-regulated, stress-responsive gene and inactivated by both epigenetic and genetic mechanisms in nasopharyngeal carcinoma. (PMID:15122337)
• Smoking under age 18 is an independent risk for BLU hypermethylation, thus identifying a molecular alteration related to the epidemiologic effect of teenage smoking as a lung cancer risk. (PMID:15540210)
• ninety-two percent of glioma tumor samples were methylated for RASSF1A, 30%-57% for BLU and 47% for MGMT, suggesting promoter methylation of these genes to be a common event in glioma tumorigenesis (PMID:18616639)
• A significant correlation between BLU methylation and loss of expression of BLU was observed in gastric, colorectal and pancreatic cancers. (PMID:20394502)
• CTCF bound to insulator sequences located between BLU and RASSF1A. (PMID:20877461)
• BLU may play a substantial role in the development and etiology of myelodysplastic syndrome. (PMID:22246278)
• The N-terminal of BLU was observed to interact with the C-terminal of SMEK1, a regulatory subunit of protein phosphatase 4. Furthermore, we determined the binding domains that are required for interaction between BLU and sMEK1. The N-terminal of BLU was observed to interact with the C-terminal of sMEK1. (PMID:22349239)
• these data indicated that methylation of the BLU promoter region is an early event during hepatocellular carcinoma development. (PMID:22766745)
• Methylation of BLU could be a potential prognostic biomarker for advanced ovarian serous carcinoma (PMID:23329649)
• Data indicate that BLU could suppress the growth of ovarian carcinoma cells through down-regulation of Bcl-2 protein. (PMID:23628417)
• ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6. (PMID:23891469)
• Mutations in ZMYND10 cause primary ciliary dyskinesia. (PMID:23891471)
• Data show that the zinc finger MYND-type containing 10 protein BLU gene may be one of the key components of signaling networks controlling tumor microenvironment and angiogenesis. (PMID:25347745)
• Data identified a novel functional BLU promoter that was regulated by Sp1. Furthermore, the hypermethylated -39 CpG in BLU proximal promoter directly reduced its binding with Sp1. (PMID:26043875)
• A novel frameshift mutation (c.367delC) in ZMYND10, unique for Slavic primary ciliary dyskinesia population (PCD), was found in homozygous state in two unrelated PCD patients. (PMID:26824761)
• BLU suppressed tumor formation by strengthening the antitumor immunity. (PMID:28029652)
• Study identified ZMYND10 as a tumor suppressor, which is downregulated in breast cancer due to its promoter hypermethylation, and suggested that ZMYND10 suppresses breast cancer metastasis by through the miR145-5p/NEDD9 signaling cascade. (PMID:31801619)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmynd10	ENSDARG00000002406
mus_musculus	Zmynd10	ENSMUSG00000010044
rattus_norvegicus	Zmynd10	ENSRNOG00000021602
drosophila_melanogaster	Zmynd10	FBGN0266709

Paralogs (2): ZMYND19 (ENSG00000165724), MSS51 (ENSG00000166343)

Protein

Protein identifiers

Zinc finger MYND domain-containing protein 10 — O75800 (reviewed: O75800)

Alternative names: Protein BLu

All UniProt accessions (3): O75800, C9JUQ8, F2Z3M9

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in axonemal structure organization and motility. Involved in axonemal pre-assembly of inner and outer dynein arms (IDA and ODA, respectively) for proper axoneme building for cilia motility. May act by indirectly regulating transcription of dynein proteins.

Subunit / interactions. Interacts (via C-terminus) with DNAAF11 (via CS domain); this interaction stabilizes DNAAF11 at the protein level. Interacts (via C-terminus) with DNAL1; this interaction stabilizes DNAL1 at the protein level. Interacts with DNAAF4, HSPA8, IQUB, RUVBL2 and DYNTL5.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriolar satellite. Apical cell membrane. Dynein axonemal particle.

Disease relevance. 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. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the ZMYND10 family.

Isoforms (2)

UniProt ID	Names	Canonical?
O75800-1	1, Lung	yes
O75800-2	2, Testis

RefSeq proteins (2): NP_001295308, NP_056980* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002893	Znf_MYND	Domain
IPR017333	UCP037948_Znf-MYND	Family
IPR052298	ZMYND10	Family

Pfam: PF01753

UniProt features (29 total): sequence variant 9, binding site 8, sequence conflict 3, strand 2, helix 2, chain 1, zinc finger region 1, splice variant 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
2D8Q	SOLUTION NMR
2DAN	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75800-F1	89.17	0.64

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 430; 394; 397; 405; 408; 414; 418; 426

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 201 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_INNER_DYNEIN_ARM_ASSEMBLY, GOBP_AXONEMAL_DYNEIN_COMPLEX_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_PROTEIN_MATURATION, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOCC_CENTROSOME, GOBP_OUTER_DYNEIN_ARM_ASSEMBLY

GO Biological Process (7): cilium movement (GO:0003341), outer dynein arm assembly (GO:0036158), inner dynein arm assembly (GO:0036159), motile cilium assembly (GO:0044458), protein localization to cilium (GO:0061512), positive regulation of motile cilium assembly (GO:1905505), protein folding (GO:0006457)

GO Molecular Function (5): zinc ion binding (GO:0008270), protein folding chaperone (GO:0044183), molecular adaptor activity (GO:0060090), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (7): cytoplasm (GO:0005737), apical plasma membrane (GO:0016324), centriolar satellite (GO:0034451), dynein axonemal particle (GO:0120293), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
axonemal dynein complex assembly	2
molecular_function	2
binding	2
intracellular membraneless organelle	2
microtubule-based movement	1
cilium assembly	1
protein localization to organelle	1
motile cilium assembly	1
positive regulation of cilium assembly	1
regulation of motile cilium assembly	1
cellular process	1
protein maturation	1
transition metal ion binding	1
protein folding	1
cation binding	1
intracellular anatomical structure	1
apical part of cell	1
plasma membrane region	1
centrosome	1
cytoplasm	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1230 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYND10	DNAAF11	Q86X45	932
ZMYND10	DNAAF5	Q86Y56	853
ZMYND10	DNAAF3	Q8N9W5	840
ZMYND10	DNAAF1	Q8NEP3	821
ZMYND10	ODAD2	Q5T2S8	809
ZMYND10	DNAAF4	Q8WXU2	799
ZMYND10	DNAAF19	Q8IW40	798
ZMYND10	SPAG1	Q07617	795
ZMYND10	RUNX1T1	Q06455	785
ZMYND10	DNAI2	Q9GZS0	776
ZMYND10	CCDC39	Q9UFE4	775
ZMYND10	RSPH4A	Q5TD94	774
ZMYND10	RSPH1	Q8WYR4	772
ZMYND10	CFAP298	P57076	769
ZMYND10	CCDC40	Q4G0X9	751

IntAct

60 interactions, top by confidence:

A	B	Type	Score
CDR1	ZMYND10	psi-mi:“MI:0915”(physical association)	0.720
ZMYND10	CDR1	psi-mi:“MI:0915”(physical association)	0.720
TSC22D4	ZMYND10	psi-mi:“MI:0915”(physical association)	0.700
ZMYND10	TSC22D4	psi-mi:“MI:0915”(physical association)	0.700
ZMYND10	NUTM1	psi-mi:“MI:0915”(physical association)	0.560
IFT43	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10		psi-mi:“MI:0915”(physical association)	0.560
NUTM1	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	TBX5	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	TCF4	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	IFT43	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	SNX11	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	EIF3M	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	WBP1	psi-mi:“MI:0915”(physical association)	0.560
FAM22F	ZMYND10	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	RBM11	psi-mi:“MI:0915”(physical association)	0.560
ZMYND10	NDUFA3	psi-mi:“MI:0915”(physical association)	0.530

BioGRID (27): ZMYND10 (Two-hybrid), TSC22D4 (Two-hybrid), IFT43 (Two-hybrid), NUTM1 (Two-hybrid), KRTAP10-3 (Two-hybrid), TSC22D4 (Two-hybrid), TSC22D4 (Affinity Capture-Western), ZMYND10 (Biochemical Activity), ZMYND10 (Affinity Capture-MS), ZMYND10 (Affinity Capture-MS), ZMYND10 (Two-hybrid), TBX5 (Two-hybrid), IFT43 (Two-hybrid), NUTM2F (Two-hybrid), MTUS2 (Two-hybrid)

ESM2 similar proteins: A0JML8, A0JP70, A2BID5, A2CEI4, A6NNW6, A9JTS5, E7FAW3, F1QNV4, O75153, O75800, O95248, P0CI65, P56192, P97874, Q08CY4, Q0VC30, Q14689, Q17QN2, Q1LWH4, Q1LXZ7, Q29S07, Q2T9L8, Q32PH0, Q3B7U4, Q3U308, Q3UAW9, Q3UH60, Q3UY23, Q4R4F1, Q641Y9, Q68FL6, Q6DG91, Q6GPP1, Q6PJN8, Q6TEN6, Q6ZNJ1, Q6ZPE2, Q6ZQA0, Q7T006, Q8BWT5

Diamond homologs: F1QN74, O75800, Q5FWU8, Q5RGL7, Q5ZMD2, Q6AXZ5, Q99ML0, Q9VU41, Q0E2F9, O94256

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

300 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	20
Likely pathogenic	10
Uncertain significance	123
Likely benign	111
Benign	8

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1332867	NM_015896.4(ZMYND10):c.747del (p.Ser250fs)	Pathogenic
1705506	NM_015896.4(ZMYND10):c.490C>T (p.Gln164Ter)	Pathogenic
2040816	NM_015896.4(ZMYND10):c.1A>G (p.Met1Val)	Pathogenic
2694149	NM_015896.4(ZMYND10):c.76G>T (p.Glu26Ter)	Pathogenic
2734537	NM_015896.4(ZMYND10):c.1096C>T (p.Gln366Ter)	Pathogenic
2742750	NM_015896.4(ZMYND10):c.88G>T (p.Glu30Ter)	Pathogenic
2876009	NM_015896.4(ZMYND10):c.732G>A (p.Trp244Ter)	Pathogenic
3383004	NM_015896.4(ZMYND10):c.31del (p.Glu11fs)	Pathogenic
3620893	NM_015896.4(ZMYND10):c.1046G>A (p.Trp349Ter)	Pathogenic
3722463	NM_015896.4(ZMYND10):c.383_384del (p.Glu128fs)	Pathogenic
3775188	NM_015896.4(ZMYND10):c.700+2T>C	Pathogenic
410632	NM_015896.4(ZMYND10):c.85T>C (p.Ser29Pro)	Pathogenic
4711105	NM_015896.4(ZMYND10):c.1191C>A (p.Cys397Ter)	Pathogenic
4782290	NM_015896.4(ZMYND10):c.3G>A (p.Met1Ile)	Pathogenic
66021	NM_015896.4(ZMYND10):c.47T>G (p.Val16Gly)	Pathogenic
66022	NM_015896.4(ZMYND10):c.300del (p.Phe101fs)	Pathogenic
66023	NM_015896.4(ZMYND10):c.486dup (p.Ser163fs)	Pathogenic
66024	NM_015896.4(ZMYND10):c.967C>T (p.Gln323Ter)	Pathogenic
66025	NM_015896.4(ZMYND10):c.593_594del (p.Val198fs)	Pathogenic
66026	NM_015896.4(ZMYND10):c.797T>C (p.Leu266Pro)	Pathogenic
1371306	NM_015896.4(ZMYND10):c.83G>A (p.Gly28Asp)	Likely pathogenic
1678047	NM_015896.4(ZMYND10):c.617T>A (p.Leu206Ter)	Likely pathogenic
2431468	NM_015896.4(ZMYND10):c.510+1del	Likely pathogenic
2626965	NM_015896.4(ZMYND10):c.1248-1G>T	Likely pathogenic
2631568	NM_015896.4(ZMYND10):c.668dup (p.Glu224fs)	Likely pathogenic
3255381	NM_015896.4(ZMYND10):c.967del (p.Gln323fs)	Likely pathogenic
3680265	NM_015896.4(ZMYND10):c.511-1G>A	Likely pathogenic
3723415	NM_015896.4(ZMYND10):c.1121+1G>A	Likely pathogenic
578119	NM_015896.4(ZMYND10):c.700+1G>A	Likely pathogenic
977546	NM_015896.4(ZMYND10):c.87del (p.Glu30fs)	Likely pathogenic

SpliceAI

1723 predictions. Top by Δscore:

Variant	Effect	Δscore
3:50341808:A:AC	donor_gain	1.0000
3:50341808:AC:A	donor_gain	1.0000
3:50341809:C:CC	donor_gain	1.0000
3:50341809:CC:C	donor_gain	1.0000
3:50341809:CCTT:C	donor_gain	1.0000
3:50341927:GGGAT:G	acceptor_gain	1.0000
3:50341928:GGAT:G	acceptor_gain	1.0000
3:50341929:GAT:G	acceptor_gain	1.0000
3:50341930:AT:A	acceptor_gain	1.0000
3:50341932:C:CC	acceptor_gain	1.0000
3:50341932:C:T	acceptor_loss	1.0000
3:50341933:T:C	acceptor_loss	1.0000
3:50342009:GCCTA:G	donor_loss	1.0000
3:50342010:CCTA:C	donor_loss	1.0000
3:50342011:CTA:C	donor_loss	1.0000
3:50342012:TAC:T	donor_loss	1.0000
3:50342014:C:CA	donor_loss	1.0000
3:50342185:C:CT	acceptor_gain	1.0000
3:50342186:A:T	acceptor_gain	1.0000
3:50342193:C:CT	acceptor_gain	1.0000
3:50342193:C:T	acceptor_gain	1.0000
3:50342194:A:T	acceptor_gain	1.0000
3:50342392:CTGA:C	donor_loss	1.0000
3:50342393:TGAC:T	donor_loss	1.0000
3:50342394:GACCT:G	donor_loss	1.0000
3:50342395:ACCT:A	donor_loss	1.0000
3:50342396:C:T	donor_loss	1.0000
3:50342410:C:A	donor_gain	1.0000
3:50343444:CCTGG:C	acceptor_loss	1.0000
3:50343445:C:CC	acceptor_gain	1.0000

AlphaMissense

2863 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:50343811:A:G	W81R	0.992
3:50343811:A:T	W81R	0.992
3:50343588:A:G	L116P	0.990
3:50345189:C:G	A46P	0.990
3:50342483:A:G	W263R	0.989
3:50342483:A:T	W263R	0.989
3:50343828:A:G	L75P	0.989
3:50345231:A:G	W32R	0.980
3:50345231:A:T	W32R	0.980
3:50341584:A:G	Y413H	0.977
3:50345200:A:G	L42P	0.977
3:50341607:C:G	C405S	0.976
3:50341608:A:T	C405S	0.976
3:50341598:C:G	C408S	0.975
3:50341599:A:T	C408S	0.975
3:50342464:A:G	L269P	0.974
3:50342936:A:G	W228R	0.974
3:50342936:A:T	W228R	0.974
3:50343809:C:A	W81C	0.974
3:50343809:C:G	W81C	0.974
3:50341583:T:C	Y413C	0.973
3:50343389:C:G	R143P	0.973
3:50341584:A:C	Y413D	0.972
3:50341886:A:G	W349R	0.972
3:50341886:A:T	W349R	0.972
3:50341608:A:G	C405R	0.971
3:50341464:C:A	W423C	0.967
3:50341464:C:G	W423C	0.967
3:50341583:T:G	Y413S	0.967
3:50343569:G:C	F122L	0.966

dbSNP variants (sampled 300 via entrez): RS1000415079 (3:50345879 G>C), RS1000420821 (3:50345819 A>C,G), RS1001443913 (3:50346700 C>G), RS1002314413 (3:50341697 C>A,T), RS1002366879 (3:50341010 C>G), RS1003332677 (3:50343678 C>A,G,T), RS1004298559 (3:50341759 C>A), RS1004437224 (3:50345740 C>G,T), RS1006370439 (3:50347366 C>G,T), RS1006688997 (3:50347164 T>A), RS1007301778 (3:50345823 G>A,T), RS1007601992 (3:50346187 C>T), RS1008107659 (3:50345066 G>A,C,T), RS1008584823 (3:50340845 G>C), RS1009176270 (3:50342271 G>A,C,T)

Disease associations

OMIM: gene MIM:607070 | disease phenotypes: MIM:244400, MIM:615444

GenCC curated gene-disease

Disease	Classification	Inheritance
primary ciliary dyskinesia 22	Strong	Autosomal recessive
primary ciliary dyskinesia	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
primary ciliary dyskinesia 22	Definitive	AR

Mondo (3): primary ciliary dyskinesia (MONDO:0016575), primary ciliary dyskinesia 22 (MONDO:0014192), primary ciliary dyskinesia 1 (MONDO:0009484)

Orphanet (2): Primary ciliary dyskinesia (Orphanet:244), Primary ciliary dyskinesia, Kartagener type (Orphanet:98861)

HPO phenotypes

63 total (30 of 63 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000119	Abnormality of the genitourinary system
HP:0000238	Hydrocephalus
HP:0000365	Hearing impairment
HP:0000389	Chronic otitis media
HP:0000403	Recurrent otitis media
HP:0000405	Conductive hearing impairment
HP:0000510	Rod-cone dystrophy
HP:0000750	Delayed speech and language development
HP:0000789	Infertility
HP:0000924	Abnormality of the skeletal system
HP:0001217	Clubbing
HP:0001627	Abnormal heart morphology
HP:0001651	Dextrocardia
HP:0001669	Transposition of the great arteries
HP:0001696	Situs inversus totalis
HP:0001719	Double outlet right ventricle
HP:0001742	Nasal congestion
HP:0001746	Asplenia
HP:0001748	Polysplenia
HP:0002011	Morphological central nervous system abnormality
HP:0002110	Bronchiectasis
HP:0002119	Ventriculomegaly
HP:0002205	Recurrent respiratory infections
HP:0002257	Chronic rhinitis
HP:0002566	Intestinal malrotation
HP:0002643	Neonatal respiratory distress
HP:0002878	Respiratory failure
HP:0003251	Male infertility
HP:0003593	Infantile onset

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST007559_24	Sleep duration (short sleep)	3.000000e-08
GCST010698_80	Subcortical volume (min-P)	3.000000e-24
GCST010699_110	Brain morphology (min-P)	4.000000e-08
GCST010701_52	Cortical surface area (MOSTest)	1.000000e-16
GCST010702_36	Subcortical volume (MOSTest)	1.000000e-10
GCST010703_262	Brain morphology (MOSTest)	2.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D002925	Ciliary Motility Disorders	C08.200; C09.150; C16.131.077.245.500; C16.320.184.500
D007619	Kartagener Syndrome	C08.127.384.500; C08.200.531; C08.695.501; C09.150.531; C14.240.400.280.500; C14.280.400.280.500; C16.131.077.245.500.531; C16.131.240.400.280.500; C16.131.740.501; C16.131.810.250.500; C16.320.184.500.531; C16.320.480

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, increases methylation	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	decreases expression	2
Particulate Matter	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
trichostatin A	affects cotreatment, affects expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
abrine	decreases expression	1
Decitabine	affects cotreatment, affects expression	1
Sunitinib	decreases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Diethylstilbestrol	decreases expression	1
Phthalic Acids	increases methylation	1
Testosterone	decreases expression	1
Valproic Acid	increases methylation	1
Zearalenone	decreases expression	1
Aflatoxin B1	increases methylation	1
S-Nitrosoglutathione	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A8E1	SEES3-1V human ZMYND10, clone1	Embryonic stem cell	Male
CVCL_A8E2	SEES3-1V human ZMYND10, clone2	Embryonic stem cell	Male
CVCL_A8E3	SEES3-1V human ZMYND10, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

71 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT02871778	PHASE2	COMPLETED	Clearing Lungs With ENaC Inhibition in Primary Ciliary Dyskinesia
NCT07318974	PHASE2	ACTIVE_NOT_RECRUITING	Melatonin Therapy for Improving ICSI Outcomes in Women With Diminished Ovarian Reserve
NCT05737485	PHASE1	COMPLETED	Study Evaluating the Safety and Tolerability of RCT1100 in Healthy and PCD Subjects
NCT06600425	PHASE1	COMPLETED	A Study to Assess the Safety, Tolerability, Ciliary Rescue, and Pharmacodynamics of RCT1100 in Adults With PCD
NCT06633757	PHASE1	COMPLETED	Study of Inhaled RCT1100 in Adults With PCD Caused by Pathogenic Mutations in the DNAI1 Gene to Measure Mucociliary Clearance
NCT04901715	EARLY_PHASE1	COMPLETED	Functional Studies of Novel Genes Mutated in Primary Ciliary Dyskinesia II: Genotype to Phenotype
NCT00005650	Not specified	COMPLETED	Genetic Study of Patients With Primary Ciliary Dyskinesia
NCT00323167	Not specified	COMPLETED	Rare Genetic Disorders of the Breathing Airways
NCT00368446	Not specified	COMPLETED	Genetic Disorders of Mucociliary Clearance in Nontuberculous Mycobacterial Lung Disease
NCT00450918	Not specified	COMPLETED	Evaluating Progression of and Diagnostic Tools for Primary Ciliary Dyskinesia in Children and Adolescents
NCT00608556	Not specified	COMPLETED	Dyskinesia, Heterotaxy and Congenital Heart Disease
NCT00686309	Not specified	UNKNOWN	Comparison of On-line and Off-line Measurements of Exhaled Nitric Oxide (NO)
NCT00722878	Not specified	COMPLETED	Long-term Lung Function and Disease Progression in Children With Early Onset Primary Ciliary Dyskinesia Lung Disease
NCT00739817	Not specified	UNKNOWN	Screening for Primary Ciliary Dyskinesia Using Nasal Nitric Oxide
NCT00783887	Not specified	COMPLETED	Diagnosis of Primary Ciliary Dyskinesia
NCT00807482	Not specified	RECRUITING	Pathogenesis of Primary Ciliary Dyskinesia (PCD) Lung Disease
NCT01070914	Not specified	UNKNOWN	Early Detection and Characterization of Primary Ciliary Dyskinesia
NCT01155115	Not specified	COMPLETED	Inflammatory and Microbiologic Markers in Sputum: Comparing Cystic Fibrosis With Primary Ciliary Dyskinesia
NCT01246258	Not specified	COMPLETED	Otolith Function in Patients With Primary Ciliary Dyskinesia
NCT01929356	Not specified	RECRUITING	Chest Physiotherapy and Lung Function in Primary Ciliary Dyskinesia
NCT02389049	Not specified	COMPLETED	Genetics of Primary Ciliary Dyskinesia
NCT02419365	Not specified	RECRUITING	International Primary Ciliary Dyskinesia (PCD) Registry
NCT02699177	Not specified	UNKNOWN	In Vivo Measurements of Nasal Ciliary Beat Frequency by Using Interferometry
NCT02704455	Not specified	NOT_YET_RECRUITING	Registry Study on Primary Ciliary Dyskinesia in Chinese Children
NCT03271840	Not specified	COMPLETED	Registry for Primary Ciliary Dyskinesia
NCT03279965	Not specified	UNKNOWN	MRI in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03320382	Not specified	UNKNOWN	Multiple Breath Washout, a Clinimetric Dataset
NCT03370029	Not specified	COMPLETED	Respiratory Muscle Strength, Exercise Capacity and Physical Activity Levels in Children Primary Ciliary Dyskinesia
NCT03494894	Not specified	COMPLETED	Bacteriological Link Between Upper and Lower Airways in Cystic Fibrosis and Primary Ciliary Dyskinesia
NCT03517865	Not specified	ACTIVE_NOT_RECRUITING	International Primary Ciliary Dyskinesia Cohort
NCT03606200	Not specified	RECRUITING	Swiss Primary Ciliary Dyskinesia Registry
NCT03704207	Not specified	RECRUITING	Utility of PCD Diagnostics to Improve Clinical Care
NCT03704896	Not specified	UNKNOWN	PRospective Observational Multicentre Study on VAriability of Lung Function in Stable PCD Patients
NCT03801395	Not specified	COMPLETED	PCD New Gene Discovery
NCT03809091	Not specified	UNKNOWN	WGS of Korean Idiopathic Bronchiectasis
NCT03832491	Not specified	COMPLETED	Effect of Game Based Approach on Oxygenation, Functional Capacity and Quality of Life in Primary Ciliary Dyskinesia
NCT04161313	Not specified	COMPLETED	Respiratory Function, Exercise Capacity and Peripheral Muscle Strength Among Patients With CF, PCD and Healthy Children
NCT04476433	Not specified	COMPLETED	Intervention in Chronic Pediatric Patients and Their Families.
NCT04489472	Not specified	UNKNOWN	The Effect of a Dietary Supplement Rich in Nitric Oxide in Patients Diagnosed With Primary Ciliary Dyskinesia.
NCT04602481	Not specified	RECRUITING	Living With Primary Ciliary Dyskinesia (Living With PCD)