ZMYND12

Summary

ZMYND12 (zinc finger MYND-type containing 12, HGNC:21192) is a protein-coding gene on chromosome 1p34.2, encoding Zinc finger MYND domain-containing protein 12 (Q9H0C1). Required for sperm flagellum function and male fertility.

Predicted to enable zinc ion binding activity. Involved in sperm axoneme assembly. Located in sperm flagellum.

Source: NCBI Gene 84217 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total — 1 pathogenic
• MANE Select transcript: NM_032257

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21192
Approved symbol	ZMYND12
Name	zinc finger MYND-type containing 12
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434N2435
Ensembl gene	ENSG00000066185
Ensembl biotype	protein_coding
Entrez	84217

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000372565, ENST00000461083, ENST00000475426, ENST00000611861, ENST00000862983

RefSeq mRNA: 2 — MANE Select: NM_032257 NM_001146192, NM_032257

CCDS: CCDS467

Canonical transcript exons

ENST00000372565 — 8 exons

Exon	Start	End
ENSE00000870169	42448467	42448638
ENSE00001190109	42435274	42435385
ENSE00001436149	42433143	42433288
ENSE00001896915	42430329	42430858
ENSE00003535831	42436421	42436543
ENSE00003580518	42439856	42440025
ENSE00003629184	42449918	42450059
ENSE00003682222	42455888	42456022

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 94.68.

FANTOM5 (CAGE): breadth broad, TPM avg 1.8569 / max 180.4340, expressed in 824 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11989	1.5328	720
11991	0.2864	83
11990	0.0377	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.68	gold quality
bronchial epithelial cell	CL:0002328	94.31	gold quality
bronchus	UBERON:0002185	92.81	gold quality
right uterine tube	UBERON:0001302	89.48	gold quality
left testis	UBERON:0004533	89.39	gold quality
testis	UBERON:0000473	88.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.15	gold quality
right testis	UBERON:0004534	88.06	gold quality
adult organism	UBERON:0007023	87.23	gold quality
oviduct epithelium	UBERON:0004804	86.72	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.10	gold quality
caput epididymis	UBERON:0004358	83.54	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.25	gold quality
tibialis anterior	UBERON:0001385	81.63	silver quality
mucosa of paranasal sinus	UBERON:0005030	80.43	gold quality
fallopian tube	UBERON:0003889	79.91	gold quality
ileal mucosa	UBERON:0000331	77.66	gold quality
corpus epididymis	UBERON:0004359	77.63	gold quality
epithelium of nasopharynx	UBERON:0001951	76.39	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.16	gold quality
hypothalamus	UBERON:0001898	75.73	gold quality
right adrenal gland	UBERON:0001233	75.29	gold quality
adenohypophysis	UBERON:0002196	75.13	gold quality
right adrenal gland cortex	UBERON:0035827	74.68	gold quality
adult mammalian kidney	UBERON:0000082	74.64	gold quality
pituitary gland	UBERON:0000007	74.13	gold quality
right lobe of liver	UBERON:0001114	73.94	gold quality
caudate nucleus	UBERON:0001873	73.53	gold quality
spinal cord	UBERON:0002240	73.47	gold quality
prefrontal cortex	UBERON:0000451	72.95	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting ZMYND12, 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-548P	99.98	72.25	3784
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-5697	99.39	67.74	1249
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-3938	98.72	66.07	834
HSA-MIR-374B-3P	98.63	68.24	1360
HSA-MIR-204-3P	97.80	66.84	1656
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4646-5P	97.70	66.84	1692
HSA-MIR-4314	97.50	67.30	1369
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-4264	96.35	64.76	1480
HSA-MIR-1245A	96.33	66.25	498
HSA-MIR-8079	96.33	66.11	484

Literature-anchored findings (GeneRIF, showing 1)

• Novel axonemal protein ZMYND12 interacts with TTC29 and DNAH1, and is required for male fertility and flagellum function. (PMID:37934199)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zmynd12	ENSDARG00000017055
mus_musculus	Zmynd12	ENSMUSG00000070806
rattus_norvegicus	Zmynd12	ENSRNOG00000022199

Paralogs (2): PDCD2 (ENSG00000071994), PDCD2L (ENSG00000126249)

Protein

Protein identifiers

Zinc finger MYND domain-containing protein 12 — Q9H0C1 (reviewed: Q9H0C1)

All UniProt accessions (3): Q9H0C1, A0A087WUN3, A0A087WZE7

UniProt curated annotations — full annotation on UniProt →

Function. Required for sperm flagellum function and male fertility.

Subcellular location. Cell projection. Cilium. Flagellum.

Tissue specificity. Expressed predominantly in the testis.

Disease relevance. Loss-of-function variants in ZMYND12 may play a role in male infertility characterized by severe asthenozoospermia with over 5% of the spermatozoa displaying flagellar abnormalities such as short, absent, coiled, bent, or irregular flagella.

RefSeq proteins (2): NP_001139664, NP_115633* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002893	Znf_MYND	Domain
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR053248	Zinc_finger_MYND_domain	Family

Pfam: PF01753

UniProt features (16 total): binding site 8, repeat 2, sequence variant 2, sequence conflict 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H0C1-F1	90.59	0.74

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): 50; 54; 17; 20; 28; 31; 37; 41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): FXR_IR1_Q6, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_MALE_GAMETE_GENERATION, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, USF_01, chr1p34, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_MICROTUBULE_BUNDLE_FORMATION, GATA1_03, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, USF_02

GO Biological Process (2): sperm axoneme assembly (GO:0007288), flagellated sperm motility (GO:0030317)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (4): sperm flagellum (GO:0036126), cilium (GO:0005929), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	1
axoneme assembly	1
sperm flagellum assembly	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
transition metal ion binding	1
binding	1
cation binding	1
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1
cellular anatomical structure	1

Protein interactions and networks

STRING

222 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYND12	ARMH2	H3BNL8	654
ZMYND12	DYDC1	Q8WWB3	512
ZMYND12	CACYBP	Q9HB71	497
ZMYND12	CCDC150	Q8NCX0	480
ZMYND12	ZNF497	Q6ZNH5	479
ZMYND12	ZNF34	Q8IZ26	449
ZMYND12	LYG1	Q8N1E2	449
ZMYND12	CCDC30	Q5VVM6	447
ZMYND12	TTC29	Q8NA56	420
ZMYND12	FAM120A	Q9NZB2	419
ZMYND12	CFAP57	Q96MR6	417
ZMYND12	CIAO1	O76071	415
ZMYND12	SPEF2	Q9C093	414
ZMYND12	SCMH1	Q96GD3	403
ZMYND12	FBXL5	Q9UKA1	398

IntAct

267 interactions, top by confidence:

A	B	Type	Score
ZMYND12	THOC1	psi-mi:“MI:0915”(physical association)	0.560
ARMC8	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
THOC1	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
MAD2L2	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
PRR35	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
QARS1	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
TEPSIN	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	ZNF148	psi-mi:“MI:0915”(physical association)	0.560
BMAL1	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
NUDT22	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
THRSP	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	SPG21	psi-mi:“MI:0915”(physical association)	0.560
MSRB3	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
TTC29	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
KANK2	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
POM121	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
PPP1R18	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	CHCHD2	psi-mi:“MI:0915”(physical association)	0.560
HOXB5	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	ABI2	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	AIRIM	psi-mi:“MI:0915”(physical association)	0.560
STRA8	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
TFAP2D	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
SOHLH1	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
CWF19L2	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
LMO4	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
LMO2	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
ZMYND12	PICK1	psi-mi:“MI:0915”(physical association)	0.560
HDAC4	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560
PRKAA2	ZMYND12	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (81): ZMYND12 (Two-hybrid), ZMYND12 (Two-hybrid), ZMYND12 (Two-hybrid), ZMYND12 (Two-hybrid), ZMYND12 (Two-hybrid), HDAC4 (Two-hybrid), GPKOW (Two-hybrid), THOC1 (Two-hybrid), SPG21 (Two-hybrid), PICK1 (Two-hybrid), TXN2 (Two-hybrid), GSTZ1 (Two-hybrid), HSF4 (Two-hybrid), SH2D4A (Two-hybrid), AES (Two-hybrid)

ESM2 similar proteins: A3KMX7, A5PKL6, F1MKX4, F1R2X6, F4IVI0, O94952, P35574, P42700, P51398, P97259, Q08834, Q09328, Q14997, Q2TBQ7, Q2TBU5, Q3U1V6, Q3V3E1, Q498D5, Q4R6Y8, Q5F204, Q5I0G3, Q5IH13, Q5IH14, Q5R5S1, Q5R7E8, Q5RL51, Q5SSW2, Q6IQC7, Q6NRP2, Q6NTT6, Q6P2P2, Q6YXW6, Q8BGG7, Q8C5P5, Q8CEL2, Q8N1I0, Q8NEC7, Q8NHU2, Q8R4G6, Q8TB36

Diamond homologs: Q38DX5, Q9H0C1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	44
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
57093	GRCh38/hg38 1p34.2-34.1(chr1:40693289-44514104)x1	Pathogenic

SpliceAI

1158 predictions. Top by Δscore:

Variant	Effect	Δscore
1:42433286:CAT:C	acceptor_gain	1.0000
1:42433288:TCT:T	acceptor_loss	1.0000
1:42433289:C:CC	acceptor_gain	1.0000
1:42433290:T:A	acceptor_loss	1.0000
1:42433294:T:C	acceptor_gain	1.0000
1:42433294:T:TC	acceptor_gain	1.0000
1:42436539:TAAAT:T	acceptor_gain	1.0000
1:42436543:TCTA:T	acceptor_loss	1.0000
1:42436544:CTATA:C	acceptor_loss	1.0000
1:42439841:A:C	donor_gain	1.0000
1:42439845:A:AC	donor_gain	1.0000
1:42439899:G:C	donor_gain	1.0000
1:42440024:ACCT:A	acceptor_loss	1.0000
1:42440025:CCT:C	acceptor_loss	1.0000
1:42440026:C:A	acceptor_loss	1.0000
1:42440027:T:A	acceptor_loss	1.0000
1:42448462:CTCA:C	donor_loss	1.0000
1:42448463:TCACC:T	donor_loss	1.0000
1:42448464:CACCA:C	donor_loss	1.0000
1:42448465:A:AC	donor_gain	1.0000
1:42448465:ACCAA:A	donor_loss	1.0000
1:42448466:C:CC	donor_gain	1.0000
1:42448466:C:G	donor_loss	1.0000
1:42448634:TACTT:T	acceptor_gain	1.0000
1:42448636:CTT:C	acceptor_gain	1.0000
1:42448639:C:CC	acceptor_gain	1.0000
1:42450055:CCCCA:C	acceptor_gain	1.0000
1:42450056:CCCA:C	acceptor_gain	1.0000
1:42450056:CCCAC:C	acceptor_gain	1.0000
1:42450057:CCAC:C	acceptor_gain	1.0000

AlphaMissense

2379 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:42439923:C:G	R176P	0.996
1:42439866:A:G	L195P	0.989
1:42439879:C:G	A191P	0.987
1:42439984:C:G	A156P	0.987
1:42449952:C:G	R73P	0.986
1:42436477:C:G	A221P	0.985
1:42439914:C:T	G179E	0.985
1:42448607:G:T	A95D	0.985
1:42455916:A:G	C28R	0.985
1:42436479:A:G	L220P	0.984
1:42439915:C:G	G179R	0.984
1:42439915:C:T	G179R	0.984
1:42448559:G:T	A111D	0.984
1:42436476:G:T	A221D	0.983
1:42448482:C:G	A137P	0.983
1:42448572:C:G	A107P	0.983
1:42455949:A:G	C17R	0.981
1:42439992:A:G	L153P	0.980
1:42448571:G:T	A107D	0.980
1:42455948:C:T	C17Y	0.980
1:42448476:C:G	A139P	0.978
1:42448490:A:G	L134P	0.978
1:42455927:G:T	A24D	0.978
1:42448560:C:G	A111P	0.977
1:42439878:G:T	A191D	0.976
1:42448481:G:T	A137D	0.976
1:42455915:C:G	C28S	0.976
1:42455916:A:T	C28S	0.976
1:42448547:A:G	L115P	0.975
1:42455907:A:G	C31R	0.975

dbSNP variants (sampled 300 via entrez): RS1000004996 (1:42438845 G>A,T), RS1000071534 (1:42437414 AT>A), RS1000258260 (1:42447838 C>G), RS1000346565 (1:42432229 T>A,G), RS1000546667 (1:42456445 T>C,G), RS1000751706 (1:42452892 G>A), RS1000860421 (1:42446233 A>G), RS1000922271 (1:42450874 T>C), RS1000987071 (1:42450666 G>A,T), RS1001146650 (1:42440503 A>G), RS1001256461 (1:42444032 AT>A,ATT), RS1001334913 (1:42446468 A>G), RS1001403332 (1:42446973 T>A,G), RS1001616426 (1:42435487 C>G), RS1001669048 (1:42435173 T>A,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

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
Benzo(a)pyrene	decreases expression, increases methylation	2
Nickel	decreases expression	2
methyleugenol	decreases expression	1
propionaldehyde	increases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	affects cotreatment, increases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
jinfukang	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Dexamethasone	increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, increases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Phthalic Acids	decreases methylation	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Aflatoxin B1	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	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_A8E7	SEES3-1V human ZMYND12, clone1	Embryonic stem cell	Male
CVCL_A8E8	SEES3-1V human ZMYND12, clone2	Embryonic stem cell	Male
CVCL_A8E9	SEES3-1V human ZMYND12, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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