ZNF530

Summary

ZNF530 (zinc finger protein 530, HGNC:29297) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 530 (Q6P9A1). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 348327 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 76 total
• MANE Select transcript: NM_001321981

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29297
Approved symbol	ZNF530
Name	zinc finger protein 530
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1508
Ensembl gene	ENSG00000183647
Ensembl biotype	protein_coding
Entrez	348327

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000332854, ENST00000597700, ENST00000597864, ENST00000598297, ENST00000600619, ENST00000885825, ENST00000920882, ENST00000920883, ENST00000920884

RefSeq mRNA: 5 — MANE Select: NM_001321981 NM_001321981, NM_001387561, NM_001387562, NM_001387563, NM_020880

CCDS: CCDS12955, CCDS92698

Canonical transcript exons

ENST00000597700 — 4 exons

Exon	Start	End
ENSE00001427790	57605686	57610098
ENSE00003157338	57600728	57600779
ENSE00003487656	57604277	57604406
ENSE00003618915	57599885	57600134

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 84.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.1717 / max 45.9404, expressed in 1438 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177784	4.1717	1438

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	84.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.13	gold quality
buccal mucosa cell	CL:0002336	83.00	gold quality
apex of heart	UBERON:0002098	80.69	gold quality
oocyte	CL:0000023	80.51	gold quality
cerebellar hemisphere	UBERON:0002245	75.66	gold quality
cerebellar cortex	UBERON:0002129	75.57	gold quality
ventricular zone	UBERON:0003053	75.41	gold quality
gastrocnemius	UBERON:0001388	75.22	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.01	gold quality
muscle of leg	UBERON:0001383	74.80	gold quality
granulocyte	CL:0000094	74.59	gold quality
cerebellum	UBERON:0002037	74.57	gold quality
ganglionic eminence	UBERON:0004023	74.11	gold quality
right atrium auricular region	UBERON:0006631	74.05	gold quality
heart left ventricle	UBERON:0002084	73.74	gold quality
cardiac atrium	UBERON:0002081	73.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.36	gold quality
cortical plate	UBERON:0005343	73.03	gold quality
cardiac ventricle	UBERON:0002082	72.86	gold quality
mucosa of stomach	UBERON:0001199	72.73	gold quality
prefrontal cortex	UBERON:0000451	72.68	gold quality
heart	UBERON:0000948	71.29	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.32	gold quality
stromal cell of endometrium	CL:0002255	70.03	gold quality
skin of leg	UBERON:0001511	69.98	gold quality
left adrenal gland	UBERON:0001234	69.81	gold quality
right frontal lobe	UBERON:0002810	69.65	gold quality
putamen	UBERON:0001874	69.64	gold quality
left adrenal gland cortex	UBERON:0035825	69.59	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.60
E-ENAD-27	no	3.96

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1981.1	ZNF530	More than 3 adjacent zinc fingers
MA1981.2	ZNF530	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:11967234

miRNA regulators (miRDB)

86 targeting ZNF530, 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-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-302A-3P	99.89	71.23	1777
HSA-MIR-302B-3P	99.89	71.23	1777
HSA-MIR-302C-3P	99.89	71.20	1778
HSA-MIR-302D-3P	99.89	71.25	1777
HSA-MIR-30D-3P	99.87	69.92	2917
HSA-MIR-30A-3P	99.87	69.74	2928
HSA-MIR-30E-3P	99.87	69.68	2942
HSA-MIR-5003-3P	99.85	69.29	2517
HSA-MIR-373-3P	99.84	70.68	1668
HSA-MIR-520E-3P	99.84	70.55	1698
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-372-3P	99.83	70.58	1691

Cross-species orthologs

0 orthologs

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF417 (ENSG00000173480), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 530 — Q6P9A1 (reviewed: Q6P9A1)

All UniProt accessions (3): Q6P9A1, M0R0Y5, M0R1P0

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

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

RefSeq proteins (5): NP_001308910, NP_001374490, NP_001374491, NP_001374492, NP_065931 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF01352

UniProt features (21 total): zinc finger region 13, sequence variant 5, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P9A1-F1	68.22	0.25

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 38 (showing top): FISCHER_DREAM_TARGETS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_DNA_BINDING_TRANSCRIPTION_REPRESSOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, HSD17B8_TARGET_GENES, LCORL_TARGET_GENES, MPHOSPH8_TARGET_GENES, NFE2L1_TARGET_GENES, TRIP13_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227), zinc ion binding (GO:0008270), DNA binding (GO:0003677), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
negative regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
negative regulation of transcription by RNA polymerase II	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription repressor activity	1
transition metal ion binding	1
nucleic acid binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

432 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF530	OR4C46	A6NHA9	507
ZNF530	ACOT6	Q3I5F7	378
ZNF530	CFAP65	Q6ZU64	372
ZNF530	TEKT5	Q96M29	370
ZNF530	ADGRF4	Q8IZF3	369
ZNF530	RCCD1	A6NED2	369
ZNF530	SAP30BP	Q9UHR5	356
ZNF530	FASTKD5	Q7L8L6	349
ZNF530	TPTE2	Q6XPS3	348
ZNF530	GPR153	Q6NV75	326
ZNF530	FAM3D	Q96BQ1	323
ZNF530	DGCR2	P98153	312
ZNF530	SLC26A8	Q96RN1	310
ZNF530	C17orf107	Q6ZR85	305
ZNF530	PLCL2	Q9UPR0	296

IntAct

2 interactions, top by confidence:

A	B	Type	Score
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): ZNF530 (Affinity Capture-MS), ZNF530 (Affinity Capture-RNA)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	11
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

806 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57604407:G:GA	donor_loss	1.0000
19:57604408:T:G	donor_loss	1.0000
19:57600135:GTGAG:G	donor_loss	0.9900
19:57600136:T:A	donor_loss	0.9900
19:57604407:G:GG	donor_gain	0.9900
19:57605680:TTTCA:T	acceptor_loss	0.9900
19:57605682:TCAG:T	acceptor_loss	0.9900
19:57605683:CAGGT:C	acceptor_loss	0.9900
19:57605684:AGGT:A	acceptor_loss	0.9900
19:57604276:GCA:G	acceptor_gain	0.9800
19:57604392:T:G	donor_gain	0.9800
19:57605684:A:AG	acceptor_gain	0.9800
19:57605685:G:GG	acceptor_gain	0.9800
19:57604271:TCATA:T	acceptor_loss	0.9700
19:57604272:CATAG:C	acceptor_loss	0.9700
19:57604273:ATAG:A	acceptor_loss	0.9700
19:57604274:TA:T	acceptor_loss	0.9700
19:57604275:A:AG	acceptor_gain	0.9700
19:57604276:G:GG	acceptor_gain	0.9700
19:57605684:AG:A	acceptor_gain	0.9700
19:57605685:GG:G	acceptor_gain	0.9700
19:57605685:GGT:G	acceptor_gain	0.9700
19:57605685:GGTT:G	acceptor_gain	0.9700
19:57604273:A:AG	acceptor_gain	0.9600
19:57604275:AGCAG:A	acceptor_gain	0.9600
19:57604276:GCAGG:G	acceptor_gain	0.9600
19:57605668:GCATT:G	acceptor_gain	0.9600
19:57600135:G:GG	donor_gain	0.9500
19:57604274:TAGCA:T	acceptor_gain	0.9500
19:57604403:CTAG:C	donor_gain	0.9500

AlphaMissense

3766 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57607191:T:C	F556L	0.998
19:57607193:T:A	F556L	0.998
19:57607193:T:G	F556L	0.998
19:57606519:T:C	F332L	0.997
19:57606521:T:A	F332L	0.997
19:57606521:T:G	F332L	0.997
19:57606435:T:C	F304L	0.996
19:57606437:T:A	F304L	0.996
19:57606437:T:G	F304L	0.996
19:57606603:T:C	F360L	0.996
19:57606605:T:A	F360L	0.996
19:57606605:T:G	F360L	0.996
19:57606771:T:C	F416L	0.996
19:57606773:T:A	F416L	0.996
19:57606773:T:G	F416L	0.996
19:57606351:T:C	F276L	0.995
19:57606353:T:A	F276L	0.995
19:57606353:T:G	F276L	0.995
19:57606939:T:C	F472L	0.995
19:57606941:T:A	F472L	0.995
19:57606941:T:G	F472L	0.995
19:57607275:T:C	F584L	0.995
19:57607277:T:A	F584L	0.995
19:57607277:T:G	F584L	0.995
19:57606687:T:C	F388L	0.994
19:57606689:T:A	F388L	0.994
19:57606689:T:G	F388L	0.994
19:57607023:T:C	F500L	0.994
19:57607025:T:A	F500L	0.994
19:57607025:T:G	F500L	0.994

dbSNP variants (sampled 300 via entrez): RS1000010023 (19:57612192 T>C), RS1000283954 (19:57603564 G>A), RS1000372417 (19:57609423 G>A), RS1000435571 (19:57609679 G>A,T), RS1000613142 (19:57603227 C>G,T), RS1001145656 (19:57605272 C>G,T), RS1001724853 (19:57611562 G>A), RS1001889160 (19:57601787 A>G), RS1002025146 (19:57600250 G>A,T), RS1002116252 (19:57608451 T>G), RS1002320593 (19:57602126 G>C), RS1002609564 (19:57598008 G>C), RS1002789107 (19:57605459 T>A,C), RS1002998279 (19:57599204 T>A), RS1003097500 (19:57612087 G>A)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
perfluorooctanoic acid	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
Leflunomide	decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Cisplatin	increases expression	1
Bucladesine	affects cotreatment, increases expression	1
Estradiol	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Niclosamide	decreases expression	1
Testosterone	affects cotreatment, decreases expression	1
Aflatoxin B1	increases expression	1
Medroxyprogesterone Acetate	affects cotreatment, increases expression	1
Okadaic Acid	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_XW60	HEK293 eGFP-ZNF530	Transformed cell line	Female

Clinical trials (associated diseases)

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