ZNF501

Summary

ZNF501 (zinc finger protein 501, HGNC:23717) is a protein-coding gene on chromosome 3p21.31, encoding Zinc finger protein 501 (Q96CX3). May be involved in transcriptional regulation.

Enables sequence-specific double-stranded DNA binding activity. Involved in Golgi organization. Located in nucleus.

Source: NCBI Gene 115560 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_001258280

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23717
Approved symbol	ZNF501
Name	zinc finger protein 501
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	MGC21738
Ensembl gene	ENSG00000186446
Ensembl biotype	protein_coding
Entrez	115560

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000396048, ENST00000484233, ENST00000486486, ENST00000620116, ENST00000927004, ENST00000927005, ENST00000927006, ENST00000927007, ENST00000927008, ENST00000954775

RefSeq mRNA: 2 — MANE Select: NM_001258280 NM_001258280, NM_145044

CCDS: CCDS2720

Canonical transcript exons

ENST00000620116 — 3 exons

Exon	Start	End
ENSE00001179362	44731476	44731560
ENSE00001549941	44734197	44737083
ENSE00001919274	44729635	44730015

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 85.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.6757 / max 88.6392, expressed in 1286 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36343	3.6757	1286

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.21	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.29	gold quality
ventricular zone	UBERON:0003053	79.59	gold quality
ganglionic eminence	UBERON:0004023	79.46	gold quality
cortical plate	UBERON:0005343	79.23	gold quality
calcaneal tendon	UBERON:0003701	78.56	gold quality
endometrium	UBERON:0001295	74.45	gold quality
islet of Langerhans	UBERON:0000006	73.23	gold quality
corpus callosum	UBERON:0002336	72.55	gold quality
smooth muscle tissue	UBERON:0001135	72.53	gold quality
stromal cell of endometrium	CL:0002255	72.23	gold quality
muscle tissue	UBERON:0002385	71.23	gold quality
skeletal muscle tissue	UBERON:0001134	71.13	gold quality
colonic epithelium	UBERON:0000397	71.06	gold quality
placenta	UBERON:0001987	70.35	gold quality
urinary bladder	UBERON:0001255	70.11	gold quality
pancreas	UBERON:0001264	69.50	gold quality
body of uterus	UBERON:0009853	69.43	gold quality
right coronary artery	UBERON:0001625	69.24	gold quality
fallopian tube	UBERON:0003889	69.24	gold quality
myometrium	UBERON:0001296	69.19	gold quality
lower esophagus muscularis layer	UBERON:0035833	69.17	gold quality
lower esophagus	UBERON:0013473	69.12	gold quality
muscle layer of sigmoid colon	UBERON:0035805	69.08	gold quality
lymph node	UBERON:0000029	68.88	gold quality
descending thoracic aorta	UBERON:0002345	68.50	gold quality
left coronary artery	UBERON:0001626	68.34	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	68.06	gold quality
popliteal artery	UBERON:0002250	67.86	gold quality
tibial artery	UBERON:0007610	67.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting ZNF501, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3688-3P	99.97	72.02	2834
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
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 501 — Q96CX3 (reviewed: Q96CX3)

Alternative names: Zinc finger protein 52

All UniProt accessions (1): Q96CX3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation. Essential for Golgi structural integrity.

Subcellular location. Nucleus. Nucleolus.

Induction. Up-regulated by Golgi stress-inducing agent nigericin.

Miscellaneous. May be due to exon skipping.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96CX3-1	1	yes
Q96CX3-2	2

RefSeq proteins (2): NP_001245209, NP_659481 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (13 total): zinc finger region 9, sequence variant 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96CX3-F1	90.88	0.89

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_GOLGI_ORGANIZATION, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, chr3p21, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CBX5_TARGET_GENES, DIDO1_TARGET_GENES, HES4_TARGET_GENES, HHEX_TARGET_GENES, SNIP1_TARGET_GENES, ZNF423_TARGET_GENES, ZNF561_TARGET_GENES

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), Golgi organization (GO:0007030)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	1
organelle organization	1
endomembrane system organization	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
cis-regulatory region sequence-specific DNA binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF501	TRIM28	Q13263	981
ZNF501	ZUP1	Q96AP4	856
ZNF501	USP5	P45974	819
ZNF501	UBB	P02248	811
ZNF501	YOD1	Q5VVQ6	788
ZNF501	USP44	Q9H0E7	773
ZNF501	OTUD7A	Q8TE49	740
ZNF501	ZPR1	O75312	670
ZNF501	SETDB1	Q15047	669
ZNF501	CRBN	Q96SW2	660
ZNF501	HDAC6	Q9UBN7	653
ZNF501	UBA2	Q9UBT2	647
ZNF501	PHF20	Q9BVI0	638
ZNF501	NPLOC4	Q8TAT6	568
ZNF501	ZFAND5	O76080	558

IntAct

5 interactions, top by confidence:

A	B	Type	Score
ZNF501	THUMPD3	psi-mi:“MI:0914”(association)	0.530
M	ZNF501	psi-mi:“MI:0915”(physical association)	0.400
ZNF501	PCK1	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): RPL26L1 (Affinity Capture-MS), RAD18 (Affinity Capture-MS), THUMPD3 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), RAD18 (Affinity Capture-MS), THUMPD3 (Affinity Capture-MS), RPL26L1 (Affinity Capture-MS), RAD18 (Affinity Capture-MS), THUMPD3 (Affinity Capture-MS), ARIH1 (Affinity Capture-MS), MRRF (Affinity Capture-MS), PCK1 (Affinity Capture-MS), ZNF501 (Affinity Capture-MS)

ESM2 similar proteins: O73694, P18712, P18717, P18719, P18720, P18721, P18722, P18724, P18727, P18730, P18731, P18732, P18734, P18735, P18738, P18740, P18741, P18742, P18743, P18744, P18750, P24399, P26634, P26635, P31507, P31508, P31509, Q01779, Q01792, Q01793, Q01797, Q01799, Q01800, Q01871, Q01872, Q02025, Q02026, Q02027, Q02034, Q02035

Diamond homologs: Q5RF70, Q96CX3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

386 predictions. Top by Δscore:

Variant	Effect	Δscore
3:44729661:GGACC:G	donor_gain	0.9900
3:44729662:GACC:G	donor_gain	0.9900
3:44729779:G:GT	donor_gain	0.9900
3:44729779:G:T	donor_gain	0.9900
3:44729786:G:GT	donor_gain	0.9900
3:44731474:A:AG	acceptor_gain	0.9900
3:44731475:G:GG	acceptor_gain	0.9900
3:44729689:G:T	donor_gain	0.9700
3:44729713:G:GT	donor_gain	0.9600
3:44729857:A:T	donor_gain	0.9600
3:44731475:GT:G	acceptor_gain	0.9600
3:44729713:G:T	donor_gain	0.9500
3:44729662:G:T	donor_gain	0.9200
3:44729723:G:GG	donor_gain	0.9200
3:44734196:G:C	acceptor_gain	0.9200
3:44729921:GCAT:G	donor_gain	0.9100
3:44730016:G:GG	donor_gain	0.9100
3:44729650:G:T	donor_gain	0.9000
3:44729719:CATG:C	donor_loss	0.9000
3:44729720:ATGG:A	donor_loss	0.9000
3:44729722:GGTG:G	donor_loss	0.9000
3:44729723:GT:G	donor_loss	0.9000
3:44729724:T:TG	donor_loss	0.9000
3:44729725:GA:G	donor_loss	0.9000
3:44729828:GCC:G	donor_gain	0.9000
3:44729883:G:GT	donor_gain	0.9000
3:44734196:GA:G	acceptor_gain	0.9000
3:44734196:GAGA:G	acceptor_gain	0.9000
3:44731475:GTGC:G	acceptor_gain	0.8900
3:44734195:A:AG	acceptor_gain	0.8900

AlphaMissense

1811 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:44734932:T:C	F171L	0.996
3:44734934:T:A	F171L	0.996
3:44734934:T:G	F171L	0.996
3:44734680:T:C	F87L	0.995
3:44734682:T:A	F87L	0.995
3:44734682:T:G	F87L	0.995
3:44734764:T:C	F115L	0.995
3:44734766:T:A	F115L	0.995
3:44734766:T:G	F115L	0.995
3:44734848:T:C	F143L	0.995
3:44734850:C:A	F143L	0.995
3:44734850:C:G	F143L	0.995
3:44735016:T:C	F199L	0.995
3:44735018:C:A	F199L	0.995
3:44735018:C:G	F199L	0.995
3:44734798:G:C	R126P	0.993
3:44735100:T:C	F227L	0.992
3:44735102:C:A	F227L	0.992
3:44735102:C:G	F227L	0.992
3:44734709:T:A	H96Q	0.991
3:44734709:T:G	H96Q	0.991
3:44734961:T:A	H180Q	0.990
3:44734961:T:G	H180Q	0.990
3:44734783:T:C	L121P	0.988
3:44734793:C:A	H124Q	0.988
3:44734793:C:G	H124Q	0.988
3:44734867:T:C	L149P	0.988
3:44735184:T:C	F255L	0.988
3:44735186:T:A	F255L	0.988
3:44735186:T:G	F255L	0.988

dbSNP variants (sampled 300 via entrez): RS1000138254 (3:44730570 C>T), RS1001049637 (3:44731680 T>G), RS1001092306 (3:44731641 G>A,T), RS1001544819 (3:44732051 G>A), RS1001656802 (3:44729854 A>G), RS1001919392 (3:44730144 C>G,T), RS1002333735 (3:44735515 T>C), RS1002520793 (3:44729042 G>A), RS1002638049 (3:44728415 G>T), RS1003058172 (3:44728486 G>A), RS1003473246 (3:44733592 G>A), RS1003561344 (3:44734693 C>G,T), RS1003619128 (3:44734269 T>C), RS1003641798 (3:44729999 A>G), RS1003982766 (3:44730874 A>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

1 associations (top):

Study	Trait	p-value
GCST008103_52	Bipolar disorder	3.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects cotreatment	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
trichostatin A	decreases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
2-palmitoylglycerol	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
clothianidin	decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
bisphenol S	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	increases methylation, decreases methylation	1
Particulate Matter	increases abundance, 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_XW53	HEK293 eGFP-ZNF501	Transformed cell line	Female

Clinical trials (associated diseases)

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