ZC3HAV1L

Summary

ZC3HAV1L (ZC3HAV1 like, HGNC:22423) is a protein-coding gene on chromosome 7q34, encoding Zinc finger CCCH-type antiviral protein 1-like (Q96H79).

Located in cytosol.

Source: NCBI Gene 92092 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 54 total
• Druggable target: yes
• MANE Select transcript: NM_080660

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22423
Approved symbol	ZC3HAV1L
Name	ZC3HAV1 like
Location	7q34
Locus type	gene with protein product
Status	Approved
Aliases	MGC14289
Ensembl gene	ENSG00000146858
Ensembl biotype	protein_coding
Entrez	92092

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000275766

RefSeq mRNA: 1 — MANE Select: NM_080660 NM_080660

CCDS: CCDS5850

Canonical transcript exons

ENST00000275766 — 5 exons

Exon	Start	End
ENSE00001034760	139034543	139034678
ENSE00001034766	139028702	139028960
ENSE00001209494	139025706	139026560
ENSE00001209507	139026708	139026833
ENSE00001209512	139035653	139036042

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 83.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.6848 / max 207.5258, expressed in 1515 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
86474	9.6848	1515

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	83.28	gold quality
stromal cell of endometrium	CL:0002255	79.43	gold quality
left ovary	UBERON:0002119	77.03	gold quality
smooth muscle tissue	UBERON:0001135	76.36	gold quality
right ovary	UBERON:0002118	75.63	gold quality
right lobe of thyroid gland	UBERON:0001119	75.50	gold quality
left lobe of thyroid gland	UBERON:0001120	75.30	gold quality
right uterine tube	UBERON:0001302	75.10	gold quality
body of uterus	UBERON:0009853	75.01	gold quality
buccal mucosa cell	CL:0002336	74.07	gold quality
thyroid gland	UBERON:0002046	73.72	gold quality
islet of Langerhans	UBERON:0000006	73.70	gold quality
colonic epithelium	UBERON:0000397	73.12	gold quality
ventricular zone	UBERON:0003053	72.93	gold quality
skin of abdomen	UBERON:0001416	72.85	gold quality
ectocervix	UBERON:0012249	72.78	gold quality
endocervix	UBERON:0000458	72.62	gold quality
ovary	UBERON:0000992	72.40	gold quality
right lung	UBERON:0002167	72.25	gold quality
tibial nerve	UBERON:0001323	72.15	gold quality
ganglionic eminence	UBERON:0004023	72.13	gold quality
skin of leg	UBERON:0001511	72.05	gold quality
metanephros cortex	UBERON:0010533	71.70	gold quality
left adrenal gland	UBERON:0001234	71.69	gold quality
cortical plate	UBERON:0005343	71.69	gold quality
left uterine tube	UBERON:0001303	71.65	gold quality
right adrenal gland	UBERON:0001233	71.61	gold quality
right adrenal gland cortex	UBERON:0035827	71.43	gold quality
left adrenal gland cortex	UBERON:0035825	71.27	gold quality
esophagus mucosa	UBERON:0002469	71.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

86 targeting ZC3HAV1L, 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-3064-3P	100.00	70.09	1254
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Literature-anchored findings (GeneRIF, showing 1)

• Study reports the discovery of a chimeric RNA between ZC3HAV1L and CHMP1A in human, located on chromosome 7 and 16, respectively. The fusion occurs at an exon-exon boundary, and was detected both computationally and experimentally from different cells or tissue types. (PMID:23273016)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zc3hav1l	ENSMUSG00000047749
rattus_norvegicus	Zc3hav1l	ENSRNOG00000013944

Paralogs (8): PARP12 (ENSG00000059378), ZC3HAV1 (ENSG00000105939), PARP11 (ENSG00000111224), PARP9 (ENSG00000138496), TIPARP (ENSG00000163659), PARP14 (ENSG00000173193), PARP15 (ENSG00000173200), PARP10 (ENSG00000178685)

Protein

Protein identifiers

Zinc finger CCCH-type antiviral protein 1-like — Q96H79 (reviewed: Q96H79)

All UniProt accessions (1): Q96H79

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q96H79-1	1	yes
Q96H79-2	2

RefSeq proteins (1): NP_542391* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026693	Zc3hav1-like	Family
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR041360	ZAP_HTH	Domain
IPR057602	Zfn-CCCH_PARP12	Domain

Pfam: PF18606, PF25261

UniProt features (9 total): compositionally biased region 2, splice variant 2, initiator methionine 1, chain 1, region of interest 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H79-F1	83.94	0.68

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): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, SENESE_HDAC1_TARGETS_UP, ZHANG_BREAST_CANCER_PROGENITORS_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN, JOHNSTONE_PARVB_TARGETS_3_DN, FORTSCHEGGER_PHF8_TARGETS_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, KAT2A_TARGET_GENES, ZNF711_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P, MIR7_1_3P, MIR7_2_3P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	1
cellular anatomical structure	1

Protein interactions and networks

STRING

364 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC3HAV1L	TEX47	Q8TBZ9	479
ZC3HAV1L	C7orf33	Q8WU49	475
ZC3HAV1L	SAMD4A	Q9UPU9	437
ZC3HAV1L	RBM43	Q6ZSC3	426
ZC3HAV1L	LENG9	Q96B70	420
ZC3HAV1L	RPP25	Q9BUL9	411
ZC3HAV1L	RBM26	Q5T8P6	404
ZC3HAV1L	TMEM278	A6NKF7	391
ZC3HAV1L	ZC3H12B	Q5HYM0	391
ZC3HAV1L	ZC3H7A	Q8IWR0	389
ZC3HAV1L	OAS1	P00973	380
ZC3HAV1L	ZC3H15	Q8WU90	380
ZC3HAV1L	IFIH1	Q9BYX4	365
ZC3HAV1L	TSEN2	Q8NCE0	362
ZC3HAV1L	PON1	P27169	353
ZC3HAV1L	AICDA	Q9GZX7	353

IntAct

22 interactions, top by confidence:

A	B	Type	Score
GPX7	GAK	psi-mi:“MI:0914”(association)	0.640
RABGGTB	PIPSL	psi-mi:“MI:0914”(association)	0.530
OTUB1		psi-mi:“MI:0914”(association)	0.350
OTUB1	EPM2A	psi-mi:“MI:0914”(association)	0.350
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350
KSR1	DDX39A	psi-mi:“MI:0914”(association)	0.350
LRRK2		psi-mi:“MI:0914”(association)	0.350
GABARAP		psi-mi:“MI:0914”(association)	0.350
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350
ANKRD39	UBA6	psi-mi:“MI:0914”(association)	0.350
CLEC4A	RBFOX3	psi-mi:“MI:0914”(association)	0.350
LINC01565	NDUFS6	psi-mi:“MI:0914”(association)	0.350
MTPN	PLCG1	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
HRAS	IGKV2D-24	psi-mi:“MI:0914”(association)	0.350
KRAS		psi-mi:“MI:0914”(association)	0.350
CFTR	UBA6	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (48): ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Synthetic Lethality), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS), ZC3HAV1L (Affinity Capture-MS)

ESM2 similar proteins: A5PK16, A5WW08, D2HNY3, E7F6T8, O15040, O35144, O88974, P41002, P53349, P97432, Q14596, Q15047, Q15554, Q3V3A7, Q501R9, Q5F479, Q5FWH2, Q5FWP4, Q5RC94, Q5RF77, Q62925, Q69ZT1, Q6AYH3, Q6P1H6, Q6P256, Q6ZQM0, Q7TN31, Q7TP65, Q7TSG2, Q80TI1, Q810L3, Q86UW9, Q86XL3, Q8CIN9, Q8JZL1, Q8N9B5, Q8NFM7, Q8R3P2, Q8WZ73, Q96EP1

Diamond homologs: Q3UPF5, Q7Z2W4, Q8BFR1, Q8BZ20, Q8K3Y6, Q96H79, Q9H0J9, Q2EMV9, Q460N3, Q460N5, Q53GL7, Q8CAS9, Q8CIE4, Q54YW4, Q7Z3E1, Q8C1B2, Q8CFF0, Q9NR21

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1020 predictions. Top by Δscore:

Variant	Effect	Δscore
7:139026830:TTAT:T	acceptor_gain	1.0000
7:139026831:TAT:T	acceptor_gain	1.0000
7:139026831:TATC:T	acceptor_loss	1.0000
7:139026833:TC:T	acceptor_loss	1.0000
7:139026834:C:CC	acceptor_gain	1.0000
7:139026834:CTA:C	acceptor_loss	1.0000
7:139026835:T:C	acceptor_loss	1.0000
7:139034537:ACT:A	donor_loss	1.0000
7:139034538:CTC:C	donor_loss	1.0000
7:139034539:TCA:T	donor_loss	1.0000
7:139034540:CA:C	donor_loss	1.0000
7:139034542:CCT:C	donor_gain	1.0000
7:139026829:ATTAT:A	acceptor_gain	0.9900
7:139026832:AT:A	acceptor_gain	0.9900
7:139028613:A:AC	donor_gain	0.9900
7:139028614:C:CC	donor_gain	0.9900
7:139028633:A:AC	donor_gain	0.9900
7:139028634:C:CC	donor_gain	0.9900
7:139028634:CTT:C	donor_gain	0.9900
7:139028696:TCCTA:T	donor_loss	0.9900
7:139028697:CCTA:C	donor_loss	0.9900
7:139028698:CTACC:C	donor_loss	0.9900
7:139028699:TAC:T	donor_loss	0.9900
7:139028700:ACCT:A	donor_loss	0.9900
7:139028701:CCTGT:C	donor_loss	0.9900
7:139028782:AGT:A	donor_gain	0.9900
7:139028784:T:TA	donor_gain	0.9900
7:139034536:GACTC:G	donor_loss	0.9900
7:139034541:A:AC	donor_gain	0.9900
7:139034542:C:CC	donor_gain	0.9900

AlphaMissense

1948 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:139028882:A:G	C194R	0.999
7:139028957:A:G	C169R	0.999
7:139028881:C:G	C194S	0.998
7:139028882:A:T	C194S	0.998
7:139028918:A:G	C182R	0.998
7:139028880:G:C	C194W	0.997
7:139028881:C:T	C194Y	0.997
7:139028888:G:C	H192D	0.997
7:139028900:A:G	C188R	0.997
7:139028916:G:C	C182W	0.997
7:139028917:C:G	C182S	0.997
7:139028917:C:T	C182Y	0.997
7:139028918:A:T	C182S	0.997
7:139028955:A:C	C169W	0.997
7:139028956:C:G	C169S	0.997
7:139028956:C:T	C169Y	0.997
7:139028957:A:T	C169S	0.997
7:139034657:A:C	H129Q	0.997
7:139034657:A:T	H129Q	0.997
7:139035695:C:T	C108Y	0.997
7:139035696:A:G	C108R	0.997
7:139035747:A:G	C91R	0.997
7:139035767:G:T	A84D	0.997
7:139035871:G:C	F49L	0.997
7:139035871:G:T	F49L	0.997
7:139035872:A:G	F49S	0.997
7:139035873:A:G	F49L	0.997
7:139028917:C:A	C182F	0.996
7:139034564:A:C	N160K	0.996
7:139034564:A:T	N160K	0.996

dbSNP variants (sampled 300 via entrez): RS1000028558 (7:139022820 G>A,C), RS1000080852 (7:139033673 T>C), RS1000083505 (7:139022537 C>T), RS1000166988 (7:139022782 G>A), RS1000217817 (7:139034063 G>A), RS1000386200 (7:139022519 T>C), RS1000693338 (7:139028224 T>C), RS1000867427 (7:139032632 GAAAT>G), RS1001085334 (7:139023870 G>A), RS1001257356 (7:139033195 T>A,C), RS1001922905 (7:139029143 C>G), RS1002009717 (7:139022151 A>G), RS1002199933 (7:139037589 C>A), RS1002361696 (7:139025051 C>T), RS1002414239 (7:139024655 T>C)

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

4 associations (top):

Study	Trait	p-value
GCST90002385_152	High light scatter reticulocyte count	2.000000e-10
GCST90002386_463	High light scatter reticulocyte percentage of red cells	4.000000e-12
GCST90002387_387	Immature fraction of reticulocytes	6.000000e-09
GCST90002406_261	Reticulocyte fraction of red cells	5.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066375 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.66	Kd	2176	nM	CHEMBL5653589
5.66	ED50	2176	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149809: Binding affinity to human ZC3HAV1L incubated for 45 mins by Kinobead based pull down assay	kd	2.1759	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, increases expression	3
bisphenol A	decreases expression, increases expression	2
sodium arsenite	decreases expression	2
Benzo(a)pyrene	decreases expression, increases methylation	2
Estradiol	increases expression	2
Tretinoin	increases expression, decreases expression	2
aristolochic acid I	decreases expression	1
2,4,6-tribromophenol	increases expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	decreases expression	1
2-butenal	decreases expression	1
butyraldehyde	increases expression	1
tetrabromobisphenol A	decreases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
pentabrominated diphenyl ether 100	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
Sunitinib	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Caffeine	decreases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Indomethacin	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652851	Binding	Binding affinity to human ZC3HAV1L incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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