ZNF280C

Summary

ZNF280C (zinc finger protein 280C, HGNC:25955) is a protein-coding gene on chromosome Xq26.1, encoding Zinc finger protein 280C (Q8ND82). May function as a transcription factor.

This gene encodes a member of the zinc finger domain-containing protein family. This family member contains multiple Cys2-His2(C2H2)-type zinc finger domains, the most common type of zinc finger domain that self-folds to form a beta-beta-alpha structure that binds a zinc ion.

Source: NCBI Gene 55609 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 172 total
• MANE Select transcript: NM_017666

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25955
Approved symbol	ZNF280C
Name	zinc finger protein 280C
Location	Xq26.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20095, ZNF633, ZPET
Ensembl gene	ENSG00000056277
Ensembl biotype	protein_coding
Entrez	55609

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000370978, ENST00000447817, ENST00000930023

RefSeq mRNA: 1 — MANE Select: NM_017666 NM_017666

CCDS: CCDS14622

Canonical transcript exons

ENST00000370978 — 19 exons

Exon	Start	End
ENSE00000676687	130230510	130230727
ENSE00000676690	130239582	130239693
ENSE00000869688	130215791	130216101
ENSE00000869690	130220349	130220480
ENSE00000869699	130236214	130236320
ENSE00000869702	130243563	130243699
ENSE00000869703	130243800	130243865
ENSE00001267218	130205117	130205153
ENSE00001267265	130236469	130236639
ENSE00001321169	130246859	130247005
ENSE00001342123	130260419	130260465
ENSE00001342132	130268762	130268899
ENSE00001599202	130205297	130205415
ENSE00001645727	130228977	130229134
ENSE00001677933	130209653	130209715
ENSE00001718368	130227682	130227782
ENSE00001772959	130226759	130226905
ENSE00001933076	130202707	130204992
ENSE00003791225	130215193	130215333

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 97.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2767 / max 239.8270, expressed in 1693 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200475	6.8854	1595
200474	2.5407	1111
200473	0.5581	312
200476	0.2924	129

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.41	gold quality
oocyte	CL:0000023	95.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.78	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.30	gold quality
adrenal tissue	UBERON:0018303	77.93	gold quality
stromal cell of endometrium	CL:0002255	75.66	gold quality
ventricular zone	UBERON:0003053	75.52	gold quality
calcaneal tendon	UBERON:0003701	75.43	gold quality
oviduct epithelium	UBERON:0004804	74.96	gold quality
ganglionic eminence	UBERON:0004023	74.93	gold quality
cortical plate	UBERON:0005343	74.68	gold quality
buccal mucosa cell	CL:0002336	74.25	silver quality
corpus epididymis	UBERON:0004359	71.87	gold quality
testis	UBERON:0000473	70.43	gold quality
bone marrow cell	CL:0002092	70.28	silver quality
islet of Langerhans	UBERON:0000006	69.51	gold quality
smooth muscle tissue	UBERON:0001135	69.46	gold quality
right testis	UBERON:0004534	69.22	gold quality
ectocervix	UBERON:0012249	68.43	gold quality
endometrium	UBERON:0001295	68.37	gold quality
cauda epididymis	UBERON:0004360	68.15	silver quality
right adrenal gland cortex	UBERON:0035827	67.51	gold quality
endocervix	UBERON:0000458	67.47	gold quality
body of uterus	UBERON:0009853	67.09	gold quality
colonic epithelium	UBERON:0000397	67.07	silver quality
caput epididymis	UBERON:0004358	66.90	silver quality
vermiform appendix	UBERON:0001154	66.88	gold quality
ovary	UBERON:0000992	66.83	gold quality
left testis	UBERON:0004533	66.69	gold quality
gastrocnemius	UBERON:0001388	66.62	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-109979	no	186.21
E-ANND-3	no	5.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

122 targeting ZNF280C, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
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-3658	99.96	73.87	4379
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-613	99.91	71.50	1710
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-380-3P	99.89	70.18	1978
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-3919	99.87	69.45	2489

Literature-anchored findings (GeneRIF, showing 2)

• ZPET binds ssDNA and localizes to DNA double-strand breaks (DSBs) and stalled replication forks. (PMID:30567999)
• Zinc finger protein 280C contributes to colorectal tumorigenesis by maintaining epigenetic repression at H3K27me3-marked loci. (PMID:35605119)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp280c	ENSMUSG00000036916
rattus_norvegicus	Zfp280c	ENSRNOG00000006797

Paralogs (28): ZBTB25 (ENSG00000089775), PRDM13 (ENSG00000112238), BCL6 (ENSG00000113916), FEZF1 (ENSG00000128610), ZBTB46 (ENSG00000130584), PRDM12 (ENSG00000130711), ZNF280D (ENSG00000137871), NACC2 (ENSG00000148411), FEZF2 (ENSG00000153266), ZBTB7B (ENSG00000160685), NACC1 (ENSG00000160877), BCL6B (ENSG00000161940), GFI1 (ENSG00000162676), GFI1B (ENSG00000165702), ZBTB49 (ENSG00000168826), ZNF280A (ENSG00000169548), ZNF581 (ENSG00000171425), ZNF524 (ENSG00000171443), ZBTB26 (ENSG00000171448), ZBTB21 (ENSG00000173276), ZNF683 (ENSG00000176083), ZBTB33 (ENSG00000177485), ZBTB3 (ENSG00000185670), ZBTB6 (ENSG00000186130), ZBTB14 (ENSG00000198081), ZBTB12 (ENSG00000204366), ZNF580 (ENSG00000213015), ZNF280B (ENSG00000275004)

Protein

Protein identifiers

Zinc finger protein 280C — Q8ND82 (reviewed: Q8ND82)

Alternative names: Suppressor of hairy wing homolog 3, Zinc finger protein 633

All UniProt accessions (2): Q8ND82, Q9UJJ2

UniProt curated annotations — full annotation on UniProt →

Function. May function as a transcription factor.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_060136* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR025243	DUF4195	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050527
IPR057618	Znf_POGZ/Z280C-D-like	Domain
IPR059074	Znf-C2H2_Z280C_D	Domain

Pfam: PF13836, PF25414, PF25429

UniProt features (35 total): cross-link 16, compositionally biased region 6, zinc finger region 5, modified residue 4, region of interest 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8ND82-F1	60.29	0.15

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 (20): 80, 223, 227, 540, 5, 10, 14, 33, 55, 75, 113, 126, 167, 174, 180, 187, 273, 522, 564, 574

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 100 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, HTF_01, DODD_NASOPHARYNGEAL_CARCINOMA_UP, AACTTT_UNKNOWN, CAGCTTT_MIR320, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, HSF1_01, GCAAGAC_MIR431, chrXq26, FORTSCHEGGER_PHF8_TARGETS_UP, RAO_BOUND_BY_SALL4, STK33_DN, STK33_NOMO_DN

GO Biological Process (2): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

518 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF280C	ADNP2	Q6IQ32	456
ZNF280C	SIAE	Q9HAT2	450
ZNF280C	MPHOSPH8	Q99549	448
ZNF280C	OR4D1	Q15615	445
ZNF280C	CRYBG2	Q8N1P7	411
ZNF280C	HEATR4	Q86WZ0	399
ZNF280C	OR4P4	Q8NGL7	398
ZNF280C	NT5DC1	Q5TFE4	383
ZNF280C	NEXMIF	Q5QGS0	380
ZNF280C	PCGF6	Q9BYE7	373
ZNF280C	OR4C6	Q8NH72	371
ZNF280C	OR4S2	Q8NH73	371
ZNF280C	TMEM164	Q5U3C3	370
ZNF280C	CWC27	Q6UX04	368
ZNF280C	UHRF2	Q96PU4	355

IntAct

59 interactions, top by confidence:

A	B	Type	Score
CBX1	ZNF280C	psi-mi:“MI:0915”(physical association)	0.740
CBX3	ZNF280C	psi-mi:“MI:0915”(physical association)	0.740
RAB8B	GDI1	psi-mi:“MI:0914”(association)	0.640
ZNF280C	TSPYL2	psi-mi:“MI:0915”(physical association)	0.560
	ZNF280C	psi-mi:“MI:0915”(physical association)	0.560
GOLGA2	ZNF280C	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-6	ZNF280C	psi-mi:“MI:0915”(physical association)	0.560
CBX5	ZNF280C	psi-mi:“MI:0915”(physical association)	0.560
DAXX	TNRC18	psi-mi:“MI:0914”(association)	0.530
CBX1	ZNF292	psi-mi:“MI:0914”(association)	0.530
Cbx1		psi-mi:“MI:0914”(association)	0.350
Bcl7c	SMARCD2	psi-mi:“MI:0914”(association)	0.350
ERBB2	SURF4	psi-mi:“MI:0914”(association)	0.350
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350
CBX1	EXOC5	psi-mi:“MI:0914”(association)	0.350
H2AZ1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
HMGA1	SUPT5H	psi-mi:“MI:0914”(association)	0.350
HMGN2	NSD2	psi-mi:“MI:0914”(association)	0.350
HMGN5	SMCHD1	psi-mi:“MI:0914”(association)	0.350
NUCKS1	SMARCA5	psi-mi:“MI:0914”(association)	0.350
NUMA1	SHANK3	psi-mi:“MI:0914”(association)	0.350
PHGDH	TIMM44	psi-mi:“MI:0914”(association)	0.350
DAXX	SETD1A	psi-mi:“MI:0914”(association)	0.350
TNFRSF1B	MAP3K7	psi-mi:“MI:0914”(association)	0.350
ZNF280C	CALML3	psi-mi:“MI:0914”(association)	0.350
	PHF20L1	psi-mi:“MI:0914”(association)	0.350
CBX3	MYL12B	psi-mi:“MI:0914”(association)	0.350
PCM1	CCDC66	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (73): ZNF280C (Proximity Label-MS), ZNF280C (Proximity Label-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Proximity Label-MS), ZNF280C (Proximity Label-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Affinity Capture-MS), ZNF280C (Proximity Label-MS), ZNF280C (Affinity Capture-RNA), ZNF280C (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8HTT5, A0JPQ7, A4FV61, A4IFK0, O75151, O88974, P35689, P49140, P55265, P55266, P97432, Q02040, Q0VEE6, Q14202, Q14596, Q15047, Q15554, Q501R9, Q53GL0, Q5EAN7, Q5F3F2, Q5HYC2, Q5R6F3, Q5RC94, Q5RF77, Q5SYB0, Q642B6, Q69Z66, Q69Z99, Q6P3Z3, Q76CY8, Q810L3, Q86XL3, Q8C4S8, Q8ND82, Q8NE31, Q8WY91, Q91VL8, Q95JV5, Q96EP1

Diamond homologs: P59817, Q5PPG4, Q68FE8, Q6N043, Q6P3Y5, Q7Z3K3, Q86YH2, Q8BZH4, Q8ND82, Q99KZ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 65 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.

GO biological processes:

GO term	Partners	Fold	FDR
heterochromatin formation	5	22.0×	1e-03
rRNA processing	5	12.2×	1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2130 predictions. Top by Δscore:

Variant	Effect	Δscore
X:130205296:CCATT:C	donor_gain	1.0000
X:130205413:CCC:C	acceptor_gain	1.0000
X:130205414:CC:C	acceptor_gain	1.0000
X:130205414:CCC:C	acceptor_gain	1.0000
X:130205415:CCTA:C	acceptor_gain	1.0000
X:130209716:C:CC	acceptor_gain	1.0000
X:130215344:C:CT	acceptor_gain	1.0000
X:130215345:G:T	acceptor_gain	1.0000
X:130215941:CTTGT:C	donor_gain	1.0000
X:130216097:GTAAC:G	acceptor_gain	1.0000
X:130216102:C:CC	acceptor_gain	1.0000
X:130220334:C:CA	donor_gain	1.0000
X:130220340:CAAA:C	donor_gain	1.0000
X:130220347:A:AC	donor_gain	1.0000
X:130220348:C:CA	donor_gain	1.0000
X:130226180:T:C	donor_gain	1.0000
X:130226753:TCTCA:T	donor_loss	1.0000
X:130226754:CTCAC:C	donor_loss	1.0000
X:130226755:TCAC:T	donor_loss	1.0000
X:130226756:CACCT:C	donor_loss	1.0000
X:130226757:A:T	donor_loss	1.0000
X:130226758:C:CA	donor_loss	1.0000
X:130226903:AACC:A	acceptor_loss	1.0000
X:130227676:GTGTA:G	donor_loss	1.0000
X:130227677:TGTAC:T	donor_loss	1.0000
X:130227678:GTACC:G	donor_loss	1.0000
X:130227679:TA:T	donor_loss	1.0000
X:130227680:A:AG	donor_loss	1.0000
X:130227681:CCT:C	donor_loss	1.0000
X:130227682:C:A	donor_loss	1.0000

AlphaMissense

4904 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:130220439:A:C	F479L	1.000
X:130220439:A:T	F479L	1.000
X:130220440:A:G	F479S	1.000
X:130220441:A:G	F479L	1.000
X:130220446:A:G	L477P	1.000
X:130220462:A:G	C472R	1.000
X:130226762:A:C	H464Q	1.000
X:130226762:A:T	H464Q	1.000
X:130226764:G:C	H464D	1.000
X:130226774:A:C	H460Q	1.000
X:130226774:A:T	H460Q	1.000
X:130226776:G:C	H460D	1.000
X:130226785:A:C	Y457D	1.000
X:130226811:A:G	L448P	1.000
X:130226813:G:C	C447W	1.000
X:130226814:C:A	C447F	1.000
X:130226814:C:G	C447S	1.000
X:130226814:C:T	C447Y	1.000
X:130226815:A:G	C447R	1.000
X:130226815:A:T	C447S	1.000
X:130226816:A:C	F446L	1.000
X:130226816:A:T	F446L	1.000
X:130226818:A:G	F446L	1.000
X:130226822:A:C	C444W	1.000
X:130226823:C:G	C444S	1.000
X:130226823:C:T	C444Y	1.000
X:130226824:A:G	C444R	1.000
X:130226824:A:T	C444S	1.000
X:130226826:A:G	L443P	1.000
X:130226829:A:G	L442S	1.000

dbSNP variants (sampled 300 via entrez): RS1000093010 (X:130241959 G>C), RS1000106782 (X:130217405 G>A), RS1000137707 (X:130237031 C>T), RS1000139424 (X:130217129 A>G), RS1000240238 (X:130208899 T>G), RS1000319971 (X:130226808 T>C), RS1000445534 (X:130223808 AAAG>A), RS1000469187 (X:130234783 G>A), RS1000652300 (X:130227261 A>G), RS1000701299 (X:130248135 C>G,T), RS1000702102 (X:130243463 G>A), RS1000767635 (X:130245131 T>C,G), RS1000867756 (X:130270194 G>A), RS1000908408 (X:130251494 A>C), RS1000952740 (X:130203206 A>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

2 associations (top):

Study	Trait	p-value
GCST008839_319	Height	2.000000e-14
GCST90002405_583	Reticulocyte count	8.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007986	reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects cotreatment, decreases expression	7
Benzo(a)pyrene	affects methylation, increases methylation, increases mutagenesis	3
Acetaminophen	increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
tacedinaline	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	increases expression	1
Panobinostat	increases expression	1
Arsenic	affects methylation	1
Caffeine	increases phosphorylation	1
Catechin	affects cotreatment, decreases expression	1
Clorgyline	increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Estradiol	increases expression	1
Hydroxyurea	decreases expression	1
Potassium Dichromate	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW28	HEK293 eGFP-ZNF280C	Transformed cell line	Female

Clinical trials (associated diseases)

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