ZC2HC1A

Summary

ZC2HC1A (zinc finger C2HC-type containing 1A, HGNC:24277) is a protein-coding gene on chromosome 8q21.13, encoding Zinc finger C2HC domain-containing protein 1A (Q96GY0).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 51101 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_016010

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24277
Approved symbol	ZC2HC1A
Name	zinc finger C2HC-type containing 1A
Location	8q21.13
Locus type	gene with protein product
Status	Approved
Aliases	CGI-62
Ensembl gene	ENSG00000104427
Ensembl biotype	protein_coding
Entrez	51101

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000263849, ENST00000519307, ENST00000521176, ENST00000521873, ENST00000705981, ENST00000705982, ENST00000874954, ENST00000929973

RefSeq mRNA: 2 — MANE Select: NM_016010 NM_001362969, NM_016010

CCDS: CCDS6223, CCDS94321

Canonical transcript exons

ENST00000263849 — 9 exons

Exon	Start	End
ENSE00000697949	78698414	78698513
ENSE00001010197	78715221	78715328
ENSE00002090191	78717328	78719765
ENSE00002122530	78697407	78697506
ENSE00003994413	78686467	78686608
ENSE00003994414	78678563	78678679
ENSE00003994415	78675787	78675863
ENSE00003994419	78689222	78689373
ENSE00003994459	78666089	78666164

Expression profiles

Bgee: expression breadth ubiquitous, 279 present calls, max score 96.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.3545 / max 495.5853, expressed in 1727 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
89468	14.6137	1704
89469	8.7408	1573

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.49	gold quality
dorsal root ganglion	UBERON:0000044	95.52	gold quality
bronchial epithelial cell	CL:0002328	94.46	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.29	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.28	gold quality
epithelium of bronchus	UBERON:0002031	93.94	gold quality
bronchus	UBERON:0002185	93.78	gold quality
ganglionic eminence	UBERON:0004023	93.73	gold quality
substantia nigra pars compacta	UBERON:0001965	93.70	gold quality
nipple	UBERON:0002030	93.60	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.57	gold quality
trigeminal ganglion	UBERON:0001675	93.36	gold quality
pons	UBERON:0000988	93.03	gold quality
cervix squamous epithelium	UBERON:0006922	92.62	gold quality
substantia nigra pars reticulata	UBERON:0001966	92.52	gold quality
middle temporal gyrus	UBERON:0002771	92.17	gold quality
buccal mucosa cell	CL:0002336	92.01	gold quality
calcaneal tendon	UBERON:0003701	91.78	gold quality
sural nerve	UBERON:0015488	91.73	gold quality
superior vestibular nucleus	UBERON:0007227	91.58	gold quality
lateral globus pallidus	UBERON:0002476	91.53	gold quality
cranial nerve II	UBERON:0000941	91.27	gold quality
ventricular zone	UBERON:0003053	90.73	gold quality
ventral tegmental area	UBERON:0002691	90.58	gold quality
embryo	UBERON:0000922	90.35	gold quality
entorhinal cortex	UBERON:0002728	89.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.35	gold quality
medulla oblongata	UBERON:0001896	89.33	gold quality
epithelium of nasopharynx	UBERON:0001951	89.21	gold quality
nasopharynx	UBERON:0001728	89.19	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-89	yes	725.41
E-ANND-3	yes	9.92
E-HCAD-5	no	15.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

144 targeting ZC2HC1A, 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-5692A	100.00	74.40	6850
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-539-5P	99.93	70.30	2855

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zc2hc1a	ENSDARG00000027915
mus_musculus	Zc2hc1a	ENSMUSG00000043542
rattus_norvegicus	Zc2hc1a	ENSRNOG00000022356

Paralogs (3): ZC2HC1B (ENSG00000118491), ZNF474 (ENSG00000164185), ZNF475 (ENSG00000250803)

Protein

Protein identifiers

Zinc finger C2HC domain-containing protein 1A — Q96GY0 (reviewed: Q96GY0)

All UniProt accessions (4): Q96GY0, A0A994J504, A0A994J7X1, H0YAP0

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the ZC2HC1 family.

RefSeq proteins (2): NP_001349898, NP_057094* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026319	ZC2HC1A/B-like	Family
IPR049899	Znf_C2HC_C3H	Domain

Pfam: PF13913

UniProt features (23 total): binding site 8, modified residue 3, sequence conflict 3, compositionally biased region 3, zinc finger region 2, region of interest 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96GY0-F1	65.29	0.19

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): 34; 38; 122; 125; 137; 141; 19; 22

Post-translational modifications (3): 223, 244, 292

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 174 (showing top): GOZGIT_ESR1_TARGETS_DN, GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, HAHTOLA_SEZARY_SYNDROM_UP, TAATGTG_MIR323, WALLACE_PROSTATE_CANCER_RACE_DN, chr8q21, GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN, OKUMURA_INFLAMMATORY_RESPONSE_LPS, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, CHYLA_CBFA2T3_TARGETS_UP, JOHNSTONE_PARVB_TARGETS_1_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, FORTSCHEGGER_PHF8_TARGETS_DN

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

377 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC2HC1A	RUFY3	Q7L099	506
ZC2HC1A	EEF1AKMT3	Q96AZ1	506
ZC2HC1A	WDR83	Q9BRX9	496
ZC2HC1A	MIOS	Q9NXC5	468
ZC2HC1A	WDR59	Q6PJI9	452
ZC2HC1A	CASTOR1	Q8WTX7	439
ZC2HC1A	RPL37	P02403	428
ZC2HC1A	WDR24	Q96S15	408
ZC2HC1A	CASTOR2	A6NHX0	406
ZC2HC1A	CNN1	P51911	400
ZC2HC1A	LRRC7	Q96NW7	393
ZC2HC1A	ZNF610	Q8N9Z0	377
ZC2HC1A	PPIH	O43447	376
ZC2HC1A	SPATA31D1	Q6ZQQ2	368
ZC2HC1A	PITRM1	Q5JRX3	361

IntAct

97 interactions, top by confidence:

A	B	Type	Score
ZC2HC1A	CASTOR1	psi-mi:“MI:0915”(physical association)	0.830
CASTOR1	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.830
CASTOR1	CASTOR2	psi-mi:“MI:0914”(association)	0.710
ZC2HC1A	LASP1	psi-mi:“MI:0915”(physical association)	0.560
SP100	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
LASP1	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1A	SP100	psi-mi:“MI:0915”(physical association)	0.560
BZZ1	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1A	BZZ1	psi-mi:“MI:0915”(physical association)	0.560
CBFA2T2	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1A	EGLN3	psi-mi:“MI:0915”(physical association)	0.560
NCK2	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1A	RAD54L2	psi-mi:“MI:0915”(physical association)	0.560
EXOC8	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
YES1	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1A	MAPRE3	psi-mi:“MI:0915”(physical association)	0.560
N	RBM47	psi-mi:“MI:0914”(association)	0.530
CAPSL	DLGAP5	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
PNMA2	CCDC85C	psi-mi:“MI:0914”(association)	0.530
TUBA1A	TUBAL3	psi-mi:“MI:2364”(proximity)	0.420
WBP4	ZC2HC1A	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (72): ZC2HC1A (Two-hybrid), ZC2HC1A (Two-hybrid), GATSL3 (Two-hybrid), ZC2HC1A (Affinity Capture-MS), ZC2HC1A (Reconstituted Complex), ZC2HC1A (Proximity Label-MS), ZC2HC1A (Proximity Label-MS), ZC2HC1A (Proximity Label-MS), ZC2HC1A (Proximity Label-MS), ZC2HC1A (Proximity Label-MS), ZC2HC1A (Affinity Capture-MS), ZC2HC1A (Affinity Capture-MS), ZC2HC1A (Affinity Capture-MS), ZC2HC1A (Affinity Capture-MS), ZC2HC1A (Affinity Capture-MS)

ESM2 similar proteins: A0JMZ1, A1L209, A1L2F3, A1L3I5, A2AWT3, A4FUE7, A6QQM4, O82171, O94519, P97868, Q08AZ1, Q14CW9, Q1W1G1, Q22122, Q2HJG4, Q2YDJ0, Q32KN7, Q5EAW4, Q5PPV5, Q5REC0, Q5TFG8, Q5ZMS6, Q618K0, Q62920, Q64GL0, Q66HC1, Q6DGN6, Q6NRP6, Q6P1U3, Q6V5K9, Q7SXT7, Q7Z6E9, Q801E2, Q8BJH1, Q8CI51, Q8H100, Q8IMP6, Q8IYB5, Q8R550, Q91W18

Diamond homologs: A4FUE7, Q22122, Q32KN7, Q53FD0, Q5PPV5, Q5REC0, Q5TFG8, Q618K0, Q6AYP4, Q7SXT7, Q8BJH1, Q8CCG1, Q96GY0, Q9BGW4, Q9D534, Q5R498

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 67 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane	5	71.5×	2e-07
Transport of connexons to the plasma membrane	5	71.5×	2e-07
Gap junction trafficking and regulation	5	62.6×	3e-07
Gap junction trafficking	5	62.6×	3e-07
Post-chaperonin tubulin folding pathway	5	62.6×	3e-07
Activation of AMPK downstream of NMDARs	6	60.1×	4e-08
Formation of tubulin folding intermediates by CCT/TriC	5	55.6×	5e-07
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	5	53.7×	5e-07

GO biological processes:

GO term	Partners	Fold	FDR
microtubule cytoskeleton organization	7	14.9×	2e-04
mitotic cell cycle	6	14.1×	6e-04
cell division	9	7.3×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2077 predictions. Top by Δscore:

Variant	Effect	Δscore
8:78666779:G:GT	donor_gain	1.0000
8:78675861:TTA:T	donor_gain	1.0000
8:78675862:TA:T	donor_gain	1.0000
8:78675864:G:GG	donor_gain	1.0000
8:78678558:A:AG	acceptor_gain	1.0000
8:78678558:AACAG:A	acceptor_loss	1.0000
8:78678559:ACAG:A	acceptor_loss	1.0000
8:78678560:CAGAA:C	acceptor_loss	1.0000
8:78678561:A:AG	acceptor_gain	1.0000
8:78678561:A:C	acceptor_loss	1.0000
8:78678562:G:GG	acceptor_gain	1.0000
8:78678562:GA:G	acceptor_gain	1.0000
8:78678562:GAA:G	acceptor_gain	1.0000
8:78678562:GAAA:G	acceptor_gain	1.0000
8:78678562:GAAAA:G	acceptor_gain	1.0000
8:78678659:G:GG	donor_gain	1.0000
8:78678676:GAGG:G	donor_gain	1.0000
8:78678678:GG:G	donor_gain	1.0000
8:78678679:GG:G	donor_gain	1.0000
8:78686466:GCC:G	acceptor_gain	1.0000
8:78686466:GCCA:G	acceptor_gain	1.0000
8:78686537:C:G	donor_gain	1.0000
8:78686645:A:T	donor_gain	1.0000
8:78689218:ATAG:A	acceptor_loss	1.0000
8:78689219:TA:T	acceptor_loss	1.0000
8:78689220:A:AG	acceptor_gain	1.0000
8:78689220:AGATT:A	acceptor_loss	1.0000
8:78689221:G:GG	acceptor_gain	1.0000
8:78689371:GTG:G	donor_gain	1.0000
8:78689371:GTGGT:G	donor_loss	1.0000

AlphaMissense

2090 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:78675825:T:A	C19S	1.000
8:78675825:T:C	C19R	1.000
8:78675826:G:A	C19Y	1.000
8:78675826:G:C	C19S	1.000
8:78675834:T:A	C22S	1.000
8:78675834:T:C	C22R	1.000
8:78675835:G:A	C22Y	1.000
8:78675835:G:C	C22S	1.000
8:78675835:G:T	C22F	1.000
8:78675836:T:G	C22W	1.000
8:78675841:G:C	R24T	1.000
8:78675842:A:C	R24S	1.000
8:78675842:A:T	R24S	1.000
8:78675846:T:C	F26L	1.000
8:78675848:C:A	F26L	1.000
8:78675848:C:G	F26L	1.000
8:78678569:C:A	H34N	1.000
8:78678569:C:G	H34D	1.000
8:78678571:T:A	H34Q	1.000
8:78678571:T:G	H34Q	1.000
8:78678581:T:A	C38S	1.000
8:78678581:T:C	C38R	1.000
8:78678582:G:A	C38Y	1.000
8:78678582:G:C	C38S	1.000
8:78678582:G:T	C38F	1.000
8:78678583:C:G	C38W	1.000
8:78678614:T:A	F49I	1.000
8:78678614:T:C	F49L	1.000
8:78678614:T:G	F49V	1.000
8:78678615:T:C	F49S	1.000

dbSNP variants (sampled 300 via entrez): RS1000095322 (8:78709981 C>G,T), RS1000147829 (8:78709717 A>G), RS1000192960 (8:78682348 T>A,C), RS1000202661 (8:78714129 A>G), RS1000264177 (8:78716996 C>T), RS1000268860 (8:78703995 C>A,T), RS1000281082 (8:78702962 T>C), RS1000357365 (8:78718028 C>A,T), RS1000388443 (8:78717656 TTA>T), RS1000403356 (8:78678985 A>G), RS1000409636 (8:78668579 T>C), RS1000447918 (8:78686422 A>G,T), RS1000449745 (8:78666318 C>A,G,T), RS1000453502 (8:78671451 A>G), RS1000514946 (8:78665973 C>T)

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

8 associations (top):

Study	Trait	p-value
GCST005531_123	Multiple sclerosis	9.000000e-17
GCST005752_162	Systemic lupus erythematosus	3.000000e-08
GCST007400_11	Systemic lupus erythematosus	1.000000e-07
GCST008152_84	Weight	3.000000e-06
GCST009391_502	Metabolite levels	6.000000e-06
GCST009391_503	Metabolite levels	6.000000e-06
GCST90002394_280	Monocyte percentage of white cells	7.000000e-12
GCST90002399_199	Neutrophil percentage of white cells	5.000000e-39

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004338	body weight
EFO:0010525	propionic acid measurement
EFO:0007989	monocyte percentage of leukocytes
EFO:0007990	neutrophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	3
Valproic Acid	decreases expression, decreases methylation	3
sodium arsenite	decreases expression, affects cotreatment, increases expression	2
(+)-JQ1 compound	increases expression	2
Tretinoin	affects cotreatment, increases expression	2
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
trichostatin A	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
Resveratrol	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	decreases expression	1
Coumestrol	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Methotrexate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Selenium	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	decreases expression	1
Urethane	increases expression	1
Vitamin E	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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