ZC2HC1B

Summary

ZC2HC1B (zinc finger C2HC-type containing 1B, HGNC:21174) is a protein-coding gene on chromosome 6q24.2, encoding Zinc finger C2HC domain-containing protein 1B (Q5TFG8).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 153918 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_001013623

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21174
Approved symbol	ZC2HC1B
Name	zinc finger C2HC-type containing 1B
Location	6q24.2
Locus type	gene with protein product
Status	Approved
Aliases	dJ468K18.5
Ensembl gene	ENSG00000118491
Ensembl biotype	protein_coding
Entrez	153918

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000237275, ENST00000539295

RefSeq mRNA: 1 — MANE Select: NM_001013623 NM_001013623

CCDS: CCDS47495

Canonical transcript exons

ENST00000237275 — 8 exons

Exon	Start	End
ENSE00001620516	143938142	143938343
ENSE00003553684	143884304	143884365
ENSE00003588160	143886032	143886151
ENSE00003591001	143864474	143864567
ENSE00003654836	143886683	143886821
ENSE00003755440	143937649	143937733
ENSE00003755770	143898552	143898691
ENSE00003757639	143903044	143903152

Expression profiles

Bgee: expression breadth broad, 64 present calls, max score 92.17.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0434 / max 34.7335, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
70270	0.0363	3
70271	0.0044	3
70269	0.0027	2

Top tissues by expression

92 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	92.17	silver quality
left testis	UBERON:0004533	81.49	gold quality
testis	UBERON:0000473	80.92	gold quality
right testis	UBERON:0004534	79.81	gold quality
placenta	UBERON:0001987	49.22	gold quality
ventricular zone	UBERON:0003053	45.74	gold quality
skeletal muscle tissue	UBERON:0001134	43.50	gold quality
bone marrow cell	CL:0002092	42.86	gold quality
lower esophagus mucosa	UBERON:0035834	42.58	silver quality
vermiform appendix	UBERON:0001154	42.53	gold quality
colonic epithelium	UBERON:0000397	42.38	gold quality
muscle tissue	UBERON:0002385	41.62	gold quality
calcaneal tendon	UBERON:0003701	41.53	gold quality
endometrium	UBERON:0001295	41.41	gold quality
hindlimb stylopod muscle	UBERON:0004252	41.25	gold quality
lymph node	UBERON:0000029	40.76	gold quality
skin of abdomen	UBERON:0001416	39.41	gold quality
lower esophagus muscularis layer	UBERON:0035833	39.10	gold quality
lower esophagus	UBERON:0013473	38.92	gold quality
sural nerve	UBERON:0015488	38.68	gold quality
tonsil	UBERON:0002372	38.38	silver quality
apex of heart	UBERON:0002098	37.73	silver quality
esophagogastric junction muscularis propria	UBERON:0035841	37.32	gold quality
smooth muscle tissue	UBERON:0001135	37.04	gold quality
subcutaneous adipose tissue	UBERON:0002190	37.03	gold quality
zone of skin	UBERON:0000014	36.71	gold quality
esophagus	UBERON:0001043	36.63	gold quality
monocyte	CL:0000576	36.53	silver quality
cortical plate	UBERON:0005343	36.47	gold quality
endocervix	UBERON:0000458	36.21	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting ZC2HC1B, 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-4673	100.00	66.64	1490
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-155-5P	99.35	70.16	1509
HSA-MIR-10522-5P	99.26	68.50	2087
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-3977	98.00	68.17	1500
HSA-MIR-6815-5P	96.05	65.55	662
HSA-MIR-6865-5P	96.05	65.58	675

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zc2hc1b	ENSMUSG00000019815
rattus_norvegicus	Zc2hc1b	ENSRNOG00000042705
drosophila_melanogaster	CG30460	FBGN0050460
drosophila_melanogaster	CG42675	FBGN0261561
caenorhabditis_elegans		WBGENE00020196

Paralogs (3): ZC2HC1A (ENSG00000104427), ZNF474 (ENSG00000164185), ZNF475 (ENSG00000250803)

Protein

Protein identifiers

Zinc finger C2HC domain-containing protein 1B — Q5TFG8 (reviewed: Q5TFG8)

All UniProt accessions (1): Q5TFG8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the ZC2HC1 family.

RefSeq proteins (1): NP_001013645* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF13913

UniProt features (10 total): binding site 4, 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-Q5TFG8-F1	74.42	0.32

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 (4): 18; 21; 33; 37

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): PAX3_TARGET_GENES, MIR2052, MIR3140_3P, MIR155_5P, MIR6865_5P, MIR6815_5P, MIR6772_5P, GSE13306_TREG_VS_TCONV_DN, GSE15750_WT_VS_TRAF6KO_DAY6_EFF_CD8_TCELL_DN, DESCARTES_MAIN_FETAL_SATELLITE_CELLS, GSE37416_CTRL_VS_3H_F_TULARENSIS_LVS_NEUTROPHIL_DN, chr6q24, GSE25123_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_MACROPHAGE_DAY10_DN, GSE22611_NOD2_TRANSD_VS_CTRL_TRANSD_HEK293_MDP_STIM_2H_DN, GSE29164_CD8_TCELL_VS_CD8_TCELL_AND_IL12_TREATED_MELANOMA_DAY7_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

194 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZC2HC1B	FAM163B	P0C2L3	735
ZC2HC1B	SEC22C	Q9BRL7	666
ZC2HC1B	ZDHHC22	Q8N966	646
ZC2HC1B	LRRTM2	O43300	508
ZC2HC1B	ZNF496	Q96IT1	439
ZC2HC1B	TSC22D4	Q9Y3Q8	419
ZC2HC1B	PHACTR2	O75167	384
ZC2HC1B	SF3B5	Q9BWJ5	372
ZC2HC1B	PLAGL1	Q9UM63	372
ZC2HC1B	LTV1	Q96GA3	365
ZC2HC1B	YJEFN3	A6XGL0	348
ZC2HC1B	RNF145	Q96MT1	345
ZC2HC1B	ADAT2	Q7Z6V5	342
ZC2HC1B	FUCA2	Q9BTY2	323
ZC2HC1B	ACADS	P16219	323

IntAct

23 interactions, top by confidence:

A	B	Type	Score
NCK2	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.560
NFKBID	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.560
GABPA	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1B	NFKBID	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1B	ZGPAT	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1B	CASTOR1	psi-mi:“MI:0915”(physical association)	0.560
ZC2HC1B	TUFM	psi-mi:“MI:0915”(physical association)	0.400
CFTR	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.370
CACNG1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
REP15	MCM3AP	psi-mi:“MI:0914”(association)	0.350
OR2M7	MARCHF6	psi-mi:“MI:0914”(association)	0.350
ZC2HC1B	TUBB4A	psi-mi:“MI:0914”(association)	0.350
OR52K2	ZC2HC1B	psi-mi:“MI:0914”(association)	0.350
ZGPAT	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.000
GABPA	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.000
CASTOR1	ZC2HC1B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (27): ZC2HC1B (Two-hybrid), GABPA (Two-hybrid), NFKBID (Two-hybrid), ZGPAT (Two-hybrid), GATSL3 (Two-hybrid), ZC2HC1B (Proximity Label-MS), ZC2HC1B (Affinity Capture-MS), ZC2HC1B (Affinity Capture-MS), TUBB4A (Affinity Capture-MS), TUBB4B (Affinity Capture-MS), TUBB (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), ZC2HC1B (Affinity Capture-MS), ZC2HC1B (Affinity Capture-MS), TUBB2A (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.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1460 predictions. Top by Δscore:

Variant	Effect	Δscore
6:143886031:GGAAA:G	acceptor_gain	1.0000
6:143886147:CCAAG:C	donor_loss	1.0000
6:143886148:CAAGG:C	donor_loss	1.0000
6:143886149:AAGGT:A	donor_loss	1.0000
6:143886150:AG:A	donor_loss	1.0000
6:143886151:GG:G	donor_loss	1.0000
6:143886152:GT:G	donor_loss	1.0000
6:143886153:T:A	donor_loss	1.0000
6:143886757:GT:G	donor_gain	1.0000
6:143898545:C:G	acceptor_gain	1.0000
6:143898550:A:AG	acceptor_gain	1.0000
6:143898551:G:GA	acceptor_gain	1.0000
6:143898551:GATT:G	acceptor_gain	1.0000
6:143903043:GGGTA:G	acceptor_gain	1.0000
6:143903148:GTCAG:G	donor_gain	1.0000
6:143903150:CAGG:C	donor_loss	1.0000
6:143903150:CAGGT:C	donor_loss	1.0000
6:143903152:GGT:G	donor_loss	1.0000
6:143903153:GT:G	donor_loss	1.0000
6:143903153:GTG:G	donor_loss	1.0000
6:143903154:T:A	donor_loss	1.0000
6:143903154:T:G	donor_loss	1.0000
6:143937645:AAAG:A	acceptor_gain	1.0000
6:143937646:A:G	acceptor_gain	1.0000
6:143867018:GTA:G	donor_gain	0.9900
6:143867019:TAT:T	donor_gain	0.9900
6:143867020:ATA:A	donor_gain	0.9900
6:143886026:TTCTA:T	acceptor_loss	0.9900
6:143886028:CTA:C	acceptor_loss	0.9900
6:143886029:TA:T	acceptor_loss	0.9900

AlphaMissense

1446 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:143884348:T:C	F25L	0.925
6:143884350:T:A	F25L	0.925
6:143884350:T:G	F25L	0.925
6:143886083:T:C	F48L	0.887
6:143886085:C:A	F48L	0.887
6:143886085:C:G	F48L	0.887
6:143898584:T:C	F128L	0.777
6:143898586:T:A	F128L	0.777
6:143898586:T:G	F128L	0.777
6:143898647:T:C	F149L	0.766
6:143898649:T:A	F149L	0.766
6:143898649:T:G	F149L	0.766
6:143898617:T:C	F139L	0.754
6:143898619:C:A	F139L	0.754
6:143898619:C:G	F139L	0.754
6:143886062:T:C	F41L	0.749
6:143886064:C:A	F41L	0.749
6:143886064:C:G	F41L	0.749
6:143884349:T:C	F25S	0.710
6:143886709:G:C	W79C	0.707
6:143886709:G:T	W79C	0.707
6:143884349:T:G	F25C	0.695
6:143884344:A:C	R23S	0.687
6:143884344:A:T	R23S	0.687
6:143886728:T:C	F86L	0.676
6:143886730:T:A	F86L	0.676
6:143886730:T:G	F86L	0.676
6:143886103:A:C	R54S	0.647
6:143886103:A:T	R54S	0.647
6:143886048:T:A	I36K	0.636

dbSNP variants (sampled 300 via entrez): RS1000012741 (6:143913438 C>T), RS1000019628 (6:143916933 G>A,C), RS1000080719 (6:143925974 T>G), RS1000083456 (6:143880718 A>G), RS1000119260 (6:143927045 G>A,C,T), RS1000133848 (6:143887628 A>G), RS1000182367 (6:143887114 A>G), RS1000206287 (6:143931469 T>C,G), RS1000241657 (6:143918796 A>G,T), RS1000361289 (6:143876747 G>A), RS1000361872 (6:143893831 C>T), RS1000433487 (6:143938107 A>G), RS1000449459 (6:143864622 C>G), RS1000466911 (6:143883960 G>A), RS1000475693 (6:143885404 A>C,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

2 associations (top):

Study	Trait	p-value
GCST002594_29	Neurofibrillary tangles	3.000000e-06
GCST007637_43	Diffusing capacity of carbon monoxide	4.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006797	neurofibrillary tangles measurement
EFO:0009369	diffusing capacity of the lung for carbon monoxide

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
Nickel	decreases expression	2
benzo(e)pyrene	increases methylation	1
aflatoxin B2	decreases methylation	1
Methapyrilene	increases methylation	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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