ZCCHC18

Summary

ZCCHC18 (zinc finger CCHC-type containing 18, HGNC:32459) is a protein-coding gene on chromosome Xq22.2, encoding Zinc finger CCHC domain-containing protein 18 (P0CG32).

Predicted to enable zinc ion binding activity. Predicted to be active in nucleus.

Source: NCBI Gene 644353 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001143978

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32459
Approved symbol	ZCCHC18
Name	zinc finger CCHC-type containing 18
Location	Xq22.2
Locus type	gene with protein product
Status	Approved
Aliases	SIZN2, PNMA7B
Ensembl gene	ENSG00000166707
Ensembl biotype	protein_coding
OMIM	301122
Entrez	644353

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000422784, ENST00000423478, ENST00000537356, ENST00000603049, ENST00000605784, ENST00000650639, ENST00000910714, ENST00000926560, ENST00000926561

RefSeq mRNA: 1 — MANE Select: NM_001143978 NM_001143978

CCDS: CCDS65304

Canonical transcript exons

ENST00000650639 — 3 exons

Exon	Start	End
ENSE00001677148	104113195	104113246
ENSE00003846006	104113434	104115842
ENSE00003848770	104112523	104113001

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 88.56.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8443 / max 27.8915, expressed in 460 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
197127	0.6335	370
209768	0.2108	101

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.56	gold quality
cortical plate	UBERON:0005343	86.75	gold quality
endothelial cell	CL:0000115	84.77	silver quality
middle temporal gyrus	UBERON:0002771	83.84	gold quality
Brodmann (1909) area 23	UBERON:0013554	82.98	gold quality
ganglionic eminence	UBERON:0004023	81.17	gold quality
popliteal artery	UBERON:0002250	80.81	gold quality
tibial artery	UBERON:0007610	80.78	gold quality
ventricular zone	UBERON:0003053	79.85	gold quality
hypothalamus	UBERON:0001898	78.71	gold quality
cerebellar hemisphere	UBERON:0002245	78.57	gold quality
islet of Langerhans	UBERON:0000006	78.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.48	gold quality
cerebellar cortex	UBERON:0002129	78.38	gold quality
cerebellum	UBERON:0002037	77.90	gold quality
Brodmann (1909) area 9	UBERON:0013540	77.56	gold quality
nucleus accumbens	UBERON:0001882	77.24	gold quality
left ovary	UBERON:0002119	76.98	gold quality
right ovary	UBERON:0002118	76.84	gold quality
aorta	UBERON:0000947	76.76	gold quality
primary visual cortex	UBERON:0002436	76.70	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	76.66	gold quality
right coronary artery	UBERON:0001625	76.38	gold quality
anterior cingulate cortex	UBERON:0009835	76.26	gold quality
right frontal lobe	UBERON:0002810	76.16	gold quality
granulocyte	CL:0000094	75.43	gold quality
neocortex	UBERON:0001950	75.40	gold quality
prefrontal cortex	UBERON:0000451	75.32	gold quality
cerebral cortex	UBERON:0000956	75.19	gold quality
frontal cortex	UBERON:0001870	74.75	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.68

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting ZCCHC18, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-1284	99.67	73.56	1353
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-8077	99.17	66.67	862
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-548L	99.06	70.90	2560
HSA-MIR-4717-3P	99.06	66.34	1072
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-4752	98.71	68.04	833
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-4773	98.35	67.30	1710
HSA-MIR-211-3P	98.14	66.77	1052
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-8056	97.15	64.49	769
HSA-MIR-4448	97.04	66.22	752
HSA-MIR-6858-3P	96.37	64.41	771
HSA-MIR-2909	96.36	67.30	562

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zcchc18	ENSMUSG00000031428
mus_musculus	Zcchc12	ENSMUSG00000036699
rattus_norvegicus	Zcchc12	ENSRNOG00000013162
rattus_norvegicus	Zcchc18	ENSRNOG00000055939

Paralogs (13): MOAP1 (ENSG00000165943), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA1 (ENSG00000176903), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA5 (ENSG00000198883), PNMA8B (ENSG00000204851), PNMA6E (ENSG00000214897), PNMA6F (ENSG00000225110), PNMA6A (ENSG00000235961), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Zinc finger CCHC domain-containing protein 18 — P0CG32 (reviewed: P0CG32)

All UniProt accessions (1): P0CG32

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the ZCCHC12 family.

RefSeq proteins (1): NP_001137450* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026523	PNMA	Family
IPR048270	PNMA_C	Domain

Pfam: PF14893

UniProt features (6 total): region of interest 2, compositionally biased region 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P0CG32-F1	70.05	0.33

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 74 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN, YAMASHITA_METHYLATED_IN_PROSTATE_CANCER, CUI_TCF21_TARGETS_2_UP, GAVIN_FOXP3_TARGETS_CLUSTER_P6, LI_INDUCED_T_TO_NATURAL_KILLER_UP, chrXq22, GSE13522_WT_VS_IFNAR_KO_SKIN_DN, GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_IFNAR_KO_DN, GSE14699_NAIVE_VS_ACT_CD8_TCELL_UP, ZNF92_TARGET_GENES, MIR12136, MIR3145_3P, MIR1284, MIR4773

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), 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
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

454 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZCCHC18	KRABD2	Q6ZNG9	626
ZCCHC18	PNMA8C	A0A1B0GUJ8	621
ZCCHC18	BOD1L2	Q8IYS8	507
ZCCHC18	LONRF3	Q496Y0	480
ZCCHC18	PNMA8B	Q9ULN7	464
ZCCHC18	F5GXT2	F5GXT2	448
ZCCHC18	PNMA8A	Q86V59	431
ZCCHC18	LAMA3	Q16787	426
ZCCHC18	NYNRIN	Q9P2P1	421
ZCCHC18	DZANK1	Q9NVP4	419
ZCCHC18	CPNE9	Q8IYJ1	405
ZCCHC18	LRRC40	Q9H9A6	394
ZCCHC18	RNFT2	Q96EX2	391
ZCCHC18	WDR13	Q9H1Z4	386
ZCCHC18	C14orf132	Q9NPU4	376

IntAct

0 interactions, top by confidence:

BioGRID (4): ZCCHC18 (Affinity Capture-MS), ZCCHC18 (Negative Genetic), ZCCHC18 (Affinity Capture-RNA), ZCCHC18 (Positive Genetic)

ESM2 similar proteins: A0A1B0GUJ8, A1A5R7, A2CJ06, A7E3N2, B1H224, B8QB46, D3Z8Y2, D3ZSP7, O55036, P0CG32, P54274, P70371, Q14BQ3, Q29RJ0, Q2HJ46, Q2T9U5, Q3TTP0, Q4R8X0, Q4R9F7, Q4VA55, Q5DTT8, Q5RBH9, Q5TKR9, Q5U310, Q5ZIX8, Q6DJS0, Q6ZQF7, Q71M44, Q7Z2W4, Q7Z7J5, Q80VH0, Q80VM8, Q8BMD7, Q8BZ21, Q8CCG4, Q8CDN1, Q8JZW8, Q8ND61, Q8TE76, Q8VD24

Diamond homologs: A0A0J9YX94, A0A0J9YXQ4, A0A1B0GUJ8, A6QLK5, A7E321, P0CG32, P0CW24, Q08DL1, Q2KIT6, Q5HZA3, Q5R6R8, Q6PEW1, Q80VM8, Q86V59, Q8JZW8, Q8ND90, Q8VD24, Q8VHZ4, Q9CZA5, Q9UL41, Q9ULN7, D3YZV8, P62521, Q5DTT8, Q5R486, Q8BHK0, Q8C1C8, Q95KI4, Q96BY2, Q96PV4, Q9ERH6, Q9GMU3, Q9H0W5, Q9UL42

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

557 predictions. Top by Δscore:

Variant	Effect	Δscore
X:104112802:G:GG	donor_gain	0.9900
X:104112978:GATT:G	donor_gain	0.9900
X:104113426:C:CA	acceptor_gain	0.9900
X:104112938:G:GT	donor_gain	0.9800
X:104113427:G:A	acceptor_gain	0.9800
X:104113432:A:AG	acceptor_gain	0.9800
X:104113433:G:GG	acceptor_gain	0.9800
X:104113424:C:CA	acceptor_gain	0.9700
X:104112808:A:T	donor_gain	0.9600
X:104112997:TTAAG:T	donor_loss	0.9600
X:104112998:TAAG:T	donor_loss	0.9600
X:104112999:AAG:A	donor_loss	0.9600
X:104113001:GGTG:G	donor_loss	0.9600
X:104113002:GT:G	donor_loss	0.9600
X:104113003:T:A	donor_loss	0.9600
X:104113270:A:T	donor_gain	0.9600
X:104113433:GTCTT:G	acceptor_gain	0.9600
X:104112314:A:AC	donor_gain	0.9500
X:104112315:C:CC	donor_gain	0.9500
X:104112888:G:GG	donor_gain	0.9500
X:104112939:A:T	donor_gain	0.9500
X:104112985:G:GT	donor_gain	0.9500
X:104113574:G:GG	donor_gain	0.9500
X:104112887:A:AG	donor_gain	0.9400
X:104112995:GAT:G	donor_gain	0.9400
X:104113243:GCTG:G	donor_gain	0.9400
X:104112973:GA:G	donor_gain	0.9300
X:104112974:A:G	donor_gain	0.9300
X:104113000:AGGTG:A	donor_gain	0.9300
X:104112892:C:G	donor_gain	0.9200

AlphaMissense

2663 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:104114472:T:C	F121L	0.944
X:104114474:T:A	F121L	0.944
X:104114474:T:G	F121L	0.944
X:104114253:T:C	F48L	0.910
X:104114255:C:A	F48L	0.910
X:104114255:C:G	F48L	0.910
X:104114736:T:C	F209L	0.867
X:104114738:C:A	F209L	0.867
X:104114738:C:G	F209L	0.867
X:104114292:T:C	F61L	0.865
X:104114294:T:A	F61L	0.865
X:104114294:T:G	F61L	0.865
X:104114511:T:C	F134L	0.850
X:104114513:T:A	F134L	0.850
X:104114513:T:G	F134L	0.850
X:104114448:T:C	F113L	0.843
X:104114450:C:A	F113L	0.843
X:104114450:C:G	F113L	0.843
X:104114586:G:C	A159P	0.829
X:104115225:T:C	F372L	0.805
X:104115227:T:A	F372L	0.805
X:104115227:T:G	F372L	0.805
X:104114644:T:C	L178P	0.799
X:104114578:T:C	L156P	0.796
X:104114635:T:C	L175S	0.772
X:104114301:T:A	W64R	0.761
X:104114301:T:C	W64R	0.761
X:104114746:T:C	L212S	0.752
X:104114368:T:C	L86S	0.747
X:104114569:A:T	E153V	0.742

dbSNP variants (sampled 300 via entrez): RS1004380129 (X:104113998 T>C), RS1008475186 (X:104116062 T>C), RS1011850714 (X:104115564 T>C), RS1015663585 (X:104114022 A>G), RS1019351888 (X:104116077 T>C), RS1019701966 (X:104115750 G>A), RS1026578517 (X:104116104 C>T), RS1028135591 (X:104115644 T>G), RS1031509145 (X:104115080 C>T), RS1033615971 (X:104114106 T>A), RS1033648632 (X:104114603 C>G,T), RS1041528316 (X:104113658 A>G), RS1046836877 (X:104115495 C>A,T), RS1050034717 (X:104116019 G>C), RS1051282748 (X:104113889 T>A)

Disease associations

OMIM: gene MIM:301122 | 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
Valproic Acid	affects expression, decreases expression, decreases methylation	4
entinostat	decreases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
quercitrin	increases expression	1
trichostatin A	decreases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	increases expression	1
Catechin	affects cotreatment, decreases expression	1
Estradiol	affects cotreatment, decreases expression	1
Progesterone	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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