ZC3H7A

Summary

ZC3H7A (zinc finger CCCH-type containing 7A, HGNC:30959) is a protein-coding gene on chromosome 16p13.13, encoding Zinc finger CCCH domain-containing protein 7A (Q8IWR0). May be a specific regulator of miRNA biogenesis.

Enables miRNA binding activity. Involved in miRNA processing. Acts upstream of with a positive effect on post-transcriptional regulation of gene expression. Predicted to be located in nucleus.

Source: NCBI Gene 29066 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Tourette syndrome (No Known Disease Relationship, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 137 total
• MANE Select transcript: NM_014153

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30959
Approved symbol	ZC3H7A
Name	zinc finger CCCH-type containing 7A
Location	16p13.13
Locus type	gene with protein product
Status	Approved
Aliases	HSPC055, FLJ20318
Ensembl gene	ENSG00000122299
Ensembl biotype	protein_coding
OMIM	619819
Entrez	29066

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 9 protein_coding, 5 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000355758, ENST00000396516, ENST00000570862, ENST00000570918, ENST00000571198, ENST00000571405, ENST00000571676, ENST00000572781, ENST00000572870, ENST00000572938, ENST00000574995, ENST00000575041, ENST00000575170, ENST00000575984, ENST00000576009, ENST00000576018, ENST00000576247

RefSeq mRNA: 1 — MANE Select: NM_014153 NM_014153

CCDS: CCDS10550

Canonical transcript exons

ENST00000355758 — 23 exons

Exon	Start	End
ENSE00000829709	11761406	11761511
ENSE00000829710	11761910	11762043
ENSE00000829711	11762671	11762747
ENSE00000829712	11763478	11763659
ENSE00000829713	11765053	11765153
ENSE00001162524	11770783	11770987
ENSE00001303895	11774980	11775013
ENSE00001323585	11774236	11774519
ENSE00002669374	11797124	11797258
ENSE00003462018	11756237	11756370
ENSE00003480195	11781425	11781464
ENSE00003494605	11768315	11768501
ENSE00003500285	11769031	11769095
ENSE00003534443	11758431	11758539
ENSE00003549579	11776452	11776532
ENSE00003570661	11767417	11767578
ENSE00003608101	11782287	11782388
ENSE00003616689	11765489	11765685
ENSE00003662589	11752669	11752832
ENSE00003670513	11776320	11776358
ENSE00003674518	11779166	11779363
ENSE00003683793	11776751	11776909
ENSE00003850603	11750597	11751506

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 97.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7163 / max 229.1759, expressed in 1812 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156312	16.6852	1812
156309	0.0191	10
156308	0.0093	5
156310	0.0027	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	97.13	gold quality
secondary oocyte	CL:0000655	96.52	gold quality
right lung	UBERON:0002167	96.26	gold quality
ventricular zone	UBERON:0003053	95.83	gold quality
popliteal artery	UBERON:0002250	95.66	gold quality
tibial artery	UBERON:0007610	95.66	gold quality
left lobe of thyroid gland	UBERON:0001120	95.63	gold quality
descending thoracic aorta	UBERON:0002345	95.59	gold quality
aorta	UBERON:0000947	95.51	gold quality
left ovary	UBERON:0002119	95.51	gold quality
body of pancreas	UBERON:0001150	95.48	gold quality
tibial nerve	UBERON:0001323	95.39	gold quality
ascending aorta	UBERON:0001496	95.37	gold quality
thoracic aorta	UBERON:0001515	95.37	gold quality
tibia	UBERON:0000979	95.28	gold quality
endocervix	UBERON:0000458	95.17	gold quality
right lobe of thyroid gland	UBERON:0001119	95.17	gold quality
right ovary	UBERON:0002118	95.15	gold quality
mucosa of stomach	UBERON:0001199	95.13	gold quality
colonic epithelium	UBERON:0000397	95.12	gold quality
upper lobe of left lung	UBERON:0008952	95.10	gold quality
thyroid gland	UBERON:0002046	94.96	gold quality
left coronary artery	UBERON:0001626	94.93	gold quality
right coronary artery	UBERON:0001625	94.91	gold quality
tendon	UBERON:0000043	94.84	gold quality
monocyte	CL:0000576	94.82	gold quality
mononuclear cell	CL:0000842	94.77	gold quality
subcutaneous adipose tissue	UBERON:0002190	94.74	gold quality
body of uterus	UBERON:0009853	94.72	gold quality
upper lobe of lung	UBERON:0008948	94.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.75

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

90 targeting ZC3H7A, 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-3163	100.00	77.23	8605
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zc3h7a	ENSDARG00000102195
mus_musculus	Zc3h7a	ENSMUSG00000037965
rattus_norvegicus	Zc3h7a	ENSRNOG00000002420

Paralogs (1): ZC3H7B (ENSG00000100403)

Protein

Protein identifiers

Zinc finger CCCH domain-containing protein 7A — Q8IWR0 (reviewed: Q8IWR0)

All UniProt accessions (9): I3L1Y3, I3L282, I3L2K5, I3L2N8, I3L323, I3L382, I3L3F9, I3L3S2, Q8IWR0

UniProt curated annotations — full annotation on UniProt →

Function. May be a specific regulator of miRNA biogenesis. Binds to microRNAs MIR7-1, MIR16-2 and MIR29A hairpins recognizing the 3’-ATA(A/T)-5’ motif in the apical loop.

Subcellular location. Nucleus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IWR0-1	1	yes
Q8IWR0-2	2

RefSeq proteins (1): NP_054872* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR036855	Znf_CCCH_sf	Homologous_superfamily
IPR039691	ZC3H7A/B	Family

Pfam: PF00642

UniProt features (17 total): zinc finger region 4, repeat 3, sequence variant 2, helix 2, chain 1, splice variant 1, strand 1, turn 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2D9M	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IWR0-F1	70.18	0.22

Functional residue map

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

Post-translational modifications (1): 210

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, ONKEN_UVEAL_MELANOMA_UP, WANG_LMO4_TARGETS_DN, FOSTER_TOLERANT_MACROPHAGE_UP, ATGCTGG_MIR338, TAATTA_CHX10_01, GOMF_MIRNA_BINDING, MATSUDA_NATURAL_KILLER_DIFFERENTIATION, WANG_TUMOR_INVASIVENESS_DN, KRIEG_HYPOXIA_NOT_VIA_KDM3A, GOMF_REGULATORY_RNA_BINDING, SHEN_SMARCA2_TARGETS_UP, GSE5503_PLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE10240_IL22_VS_IL17_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP

GO Biological Process (2): post-transcriptional regulation of gene expression (GO:0010608), miRNA processing (GO:0035196)

GO Molecular Function (5): RNA binding (GO:0003723), zinc ion binding (GO:0008270), miRNA binding (GO:0035198), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of gene expression	1
regulatory ncRNA processing	1
nucleic acid binding	1
transition metal ion binding	1
regulatory RNA binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2529 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC3H7A	DEXI	O95424	588
ZC3H7A	ZNHIT6	Q9NWK9	566
ZC3H7A	MVB12A	Q96EY5	547
ZC3H7A	MEAF6	Q9HAF1	507
ZC3H7A	NUTM2A	Q8IVF1	489
ZC3H7A	EZHIP	Q86X51	482
ZC3H7A	PHF1	O43189	441
ZC3H7A	MBTD1	Q05BQ5	420
ZC3H7A	TXNDC11	Q6PKC3	408
ZC3H7A	JAZF1	Q86VZ6	395
ZC3H7A	SYNDIG1L	A6NDD5	391
ZC3H7A	ZC3HAV1L	Q96H79	389
ZC3H7A	RMI2	Q96E14	357
ZC3H7A	ZC3H4	Q9UPT8	356
ZC3H7A	LENG9	Q96B70	350

IntAct

23 interactions, top by confidence:

A	B	Type	Score
BIRC7	HTRA2	psi-mi:“MI:0914”(association)	0.640
rep	SBNO1	psi-mi:“MI:0914”(association)	0.530
HSPA12B	EEF2K	psi-mi:“MI:0914”(association)	0.530
PIP	TBKBP1	psi-mi:“MI:0914”(association)	0.530
SDC1	ILVBL	psi-mi:“MI:0915”(physical association)	0.400
ZC3H7A	STK3	psi-mi:“MI:0915”(physical association)	0.370
Rrbp1	PIPSL	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
BIRC7	HTRA2	psi-mi:“MI:0914”(association)	0.350
	NAP1L1	psi-mi:“MI:0914”(association)	0.350
rep	SBNO1	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
PIP	RBM47	psi-mi:“MI:0914”(association)	0.350
HSPA12B	VWA8	psi-mi:“MI:0914”(association)	0.350
HNRNPCL2	SMCHD1	psi-mi:“MI:0914”(association)	0.350
ZC3H7A	ACADL	psi-mi:“MI:0914”(association)	0.350
RPS3	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
ZC3H7A	PAK1	psi-mi:“MI:0915”(physical association)	0.000
COL7A1	ZC3H7A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (319): ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-RNA), ZC3H7A (Affinity Capture-MS), ZC3H7A (Affinity Capture-MS), ZC3H7A (Proximity Label-MS), UBAP2L (Proximity Label-MS), CNOT1 (Proximity Label-MS), GIGYF2 (Proximity Label-MS), ANKHD1 (Proximity Label-MS)

ESM2 similar proteins: A0JN62, A2RT67, A2RUS2, A2VDU2, A4IFB6, A4IIM3, A7MBL8, B1H2P5, B4F779, O94967, P48553, Q08CL8, Q0VEJ0, Q14161, Q15650, Q3TLI0, Q4R350, Q5RAQ5, Q5RCP7, Q5RDV5, Q5TKA1, Q5XIA4, Q5ZIW2, Q5ZJK1, Q68CZ1, Q6AYF1, Q6QD73, Q7TSG1, Q7ZYH1, Q8BH15, Q8BIK4, Q8BKH7, Q8C735, Q8CG73, Q8CGF6, Q8IWR0, Q8IZQ1, Q8N6S4, Q8N960, Q8NEU8

Diamond homologs: A4K2V0, A6HD62, D7REX8, F8RP11, O13754, O14085, O14217, O35814, O54981, P23231, P31948, P33313, Q07617, Q15785, Q2U919, Q3KRD5, Q3ZBZ8, Q43468, Q4R8N7, Q54M20, Q5R8D8, Q5WA76, Q5XEP2, Q60864, Q68F64, Q6DGE9, Q8CGY6, Q8IWR0, Q8IWX7, Q99615, Q9HGM9, Q9QYI3, Q9STH1, Q9UGR2, Q9UNE7, Q9WUD1, Q9D4H7, A0JN74, A6NGJ6, B1H278

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	105
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3035 predictions. Top by Δscore:

Variant	Effect	Δscore
16:11751504:TACCT:T	acceptor_loss	1.0000
16:11751507:C:A	acceptor_loss	1.0000
16:11751508:T:A	acceptor_loss	1.0000
16:11752664:CATA:C	donor_gain	1.0000
16:11752665:ATAC:A	donor_loss	1.0000
16:11752666:TACCT:T	donor_loss	1.0000
16:11752667:A:C	donor_loss	1.0000
16:11752668:C:CG	donor_loss	1.0000
16:11752668:CCTA:C	donor_gain	1.0000
16:11752668:CCTAT:C	donor_gain	1.0000
16:11752672:T:C	donor_gain	1.0000
16:11752688:AG:A	donor_gain	1.0000
16:11752829:CCAC:C	acceptor_gain	1.0000
16:11752830:CACC:C	acceptor_gain	1.0000
16:11752836:A:C	acceptor_gain	1.0000
16:11752842:A:T	acceptor_gain	1.0000
16:11756235:A:AC	donor_gain	1.0000
16:11756236:C:CC	donor_gain	1.0000
16:11756371:C:CC	acceptor_gain	1.0000
16:11758429:A:AC	donor_gain	1.0000
16:11758429:ACT:A	donor_gain	1.0000
16:11758429:ACTC:A	donor_gain	1.0000
16:11758430:C:CC	donor_gain	1.0000
16:11758430:CT:C	donor_gain	1.0000
16:11758430:CTC:C	donor_gain	1.0000
16:11758430:CTCC:C	donor_gain	1.0000
16:11758432:C:CA	donor_gain	1.0000
16:11758535:CACAG:C	acceptor_gain	1.0000
16:11758537:CAG:C	acceptor_gain	1.0000
16:11758540:C:CC	acceptor_gain	1.0000

AlphaMissense

6453 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:11751434:C:A	W933C	1.000
16:11751434:C:G	W933C	1.000
16:11751436:A:G	W933R	1.000
16:11751436:A:T	W933R	1.000
16:11758455:A:G	W802R	1.000
16:11758455:A:T	W802R	1.000
16:11758481:G:T	A793D	1.000
16:11758489:A:C	C790W	1.000
16:11758490:C:G	C790S	1.000
16:11758490:C:T	C790Y	1.000
16:11758491:A:G	C790R	1.000
16:11758491:A:T	C790S	1.000
16:11758508:C:G	C784S	1.000
16:11758509:A:G	C784R	1.000
16:11758509:A:T	C784S	1.000
16:11758534:G:C	C775W	1.000
16:11758535:C:G	C775S	1.000
16:11758535:C:T	C775Y	1.000
16:11758536:A:G	C775R	1.000
16:11758536:A:T	C775S	1.000
16:11761510:A:G	W739R	1.000
16:11761510:A:T	W739R	1.000
16:11761930:A:C	C731W	1.000
16:11761931:C:G	C731S	1.000
16:11761931:C:T	C731Y	1.000
16:11761932:A:G	C731R	1.000
16:11761932:A:T	C731S	1.000
16:11761979:C:G	C715S	1.000
16:11761980:A:G	C715R	1.000
16:11761980:A:T	C715S	1.000

dbSNP variants (sampled 300 via entrez): RS1000014974 (16:11780542 T>G), RS1000031665 (16:11785715 C>G,T), RS1000076753 (16:11779503 G>A), RS1000166144 (16:11791050 G>A), RS1000233847 (16:11767726 G>T), RS1000285970 (16:11773780 A>C,G), RS1000376041 (16:11790490 A>C), RS1000389525 (16:11768225 T>A,C), RS1000447753 (16:11770315 T>G), RS1000456197 (16:11792174 T>C), RS1000471386 (16:11780851 T>C), RS1000672617 (16:11771880 A>C,G), RS1000675610 (16:11796917 C>G), RS1000698198 (16:11762235 G>A,C), RS1000735179 (16:11771643 G>T)

Disease associations

OMIM: gene MIM:619819 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
Tourette syndrome	No Known Disease Relationship	Unknown

Mondo (1): Tourette syndrome (MONDO:0007661)

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST000363_8	QT interval	5.000000e-15
GCST006427_37	Depression in smokers	5.000000e-06
GCST009391_295	Metabolite levels	5.000000e-06
GCST012071_13	Response to selenium supplementation (change in plasma selenium concentration)	9.000000e-06
GCST90002398_294	Neutrophil count	6.000000e-11
GCST90002399_262	Neutrophil percentage of white cells	1.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004682	QT interval
EFO:0010425	triacylglycerol 54:7 measurement
EFO:0600021	response to dietary selenium supplementation
EFO:0004833	neutrophil count
EFO:0007990	neutrophil percentage of leukocytes

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D005879	Tourette Syndrome	C10.228.140.079.898; C10.228.662.825.800; C10.574.500.850; C16.320.400.820; F03.625.992.850

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
Lead	affects splicing, increases expression	2
Valproic Acid	affects expression, decreases expression	2
FR900359	decreases phosphorylation	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
trichostatin A	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, decreases reaction	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
perfluorooctane sulfonic acid	decreases expression	1
torcetrapib	increases expression	1
abrine	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	increases abundance, increases oxidation, affects cotreatment	1
Benzo(a)pyrene	decreases methylation	1
Caffeine	decreases phosphorylation	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nicotine	increases splicing	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Quercetin	increases expression	1
Ribonucleotides	affects binding	1
Smoke	decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tunicamycin	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_YP34	H58	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00152750	PHASE4	UNKNOWN	Study of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00226824	PHASE4	TERMINATED	Safety Study of Galantamine in Tic Disorders
NCT00241176	PHASE4	COMPLETED	Open Label Trial of Aripiprazole in Children and Adolescents With Tourette’s Disorder
NCT00370838	PHASE4	COMPLETED	Comparison of Keppra and Clonidine in the Treatment of Tics
NCT01018056	PHASE4	COMPLETED	Developing New Treatments for Tourette Syndrome: Therapeutic Trials With Modulators of Glutamatergic Neurotransmission
NCT01547000	PHASE4	COMPLETED	Guanfacine in Children With Tic Disorders
NCT03239210	PHASE4	COMPLETED	Effects of Ondansetron in Obsessive-compulsive and Tic Disorders
NCT00004376	PHASE3	COMPLETED	Phase III Randomized, Double-Blind, Placebo-Controlled Study of Guanfacine for Tourette Syndrome and Attention Deficit Hyperactivity Disorder
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