ZNF497

Summary

ZNF497 (zinc finger protein 497, HGNC:23714) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 497 (Q6ZNH5). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity 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 located in nucleus.

Source: NCBI Gene 162968 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 117 total
• MANE Select transcript: NM_198458

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23714
Approved symbol	ZNF497
Name	zinc finger protein 497
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ44773
Ensembl gene	ENSG00000174586
Ensembl biotype	protein_coding
Entrez	162968

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 17 protein_coding

ENST00000311044, ENST00000425453, ENST00000595763, ENST00000902085, ENST00000902086, ENST00000902087, ENST00000902088, ENST00000902089, ENST00000902090, ENST00000902091, ENST00000902092, ENST00000914493, ENST00000914494, ENST00000914495, ENST00000966720, ENST00000966721, ENST00000966722

RefSeq mRNA: 2 — MANE Select: NM_198458 NM_001207009, NM_198458

CCDS: CCDS12977

Canonical transcript exons

ENST00000311044 — 3 exons

Exon	Start	End
ENSE00001210500	58354357	58357649
ENSE00001376549	58362677	58362751
ENSE00003580047	58358489	58358585

Expression profiles

Bgee: expression breadth ubiquitous, 157 present calls, max score 87.02.

FANTOM5 (CAGE): breadth broad, TPM avg 1.0577 / max 15.2469, expressed in 543 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182954	1.0577	543

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	87.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	78.58	gold quality
cortical plate	UBERON:0005343	74.30	gold quality
ventricular zone	UBERON:0003053	72.63	gold quality
right hemisphere of cerebellum	UBERON:0014890	72.42	gold quality
cerebellar hemisphere	UBERON:0002245	72.20	gold quality
cerebellar cortex	UBERON:0002129	72.13	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	71.65	silver quality
ganglionic eminence	UBERON:0004023	70.31	gold quality
cerebellum	UBERON:0002037	70.06	gold quality
right lobe of thyroid gland	UBERON:0001119	69.91	gold quality
left lobe of thyroid gland	UBERON:0001120	69.64	gold quality
adenohypophysis	UBERON:0002196	69.40	gold quality
stromal cell of endometrium	CL:0002255	69.36	gold quality
pituitary gland	UBERON:0000007	68.58	gold quality
right frontal lobe	UBERON:0002810	68.15	gold quality
thyroid gland	UBERON:0002046	67.97	gold quality
metanephros cortex	UBERON:0010533	67.58	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	67.48	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.48	gold quality
nucleus accumbens	UBERON:0001882	67.22	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	66.95	gold quality
left uterine tube	UBERON:0001303	66.90	gold quality
right lobe of liver	UBERON:0001114	66.66	gold quality
islet of Langerhans	UBERON:0000006	66.58	gold quality
body of pancreas	UBERON:0001150	66.58	gold quality
endocervix	UBERON:0000458	66.54	gold quality
right ovary	UBERON:0002118	66.31	gold quality
left ovary	UBERON:0002119	65.72	gold quality
fallopian tube	UBERON:0003889	65.72	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.83

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2567.1	ZNF497	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605368

miRNA regulators (miRDB)

60 targeting ZNF497, 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-4645-5P	99.98	65.81	1284
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-30B-3P	99.70	65.76	2325
HSA-MIR-3689A-3P	99.70	65.73	2306
HSA-MIR-3689B-3P	99.70	65.71	2311
HSA-MIR-3689C	99.70	65.71	2311
HSA-MIR-6779-5P	99.70	65.76	2363
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-6762-3P	99.66	66.94	1188
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-298	99.63	67.56	1916
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-6503-5P	99.62	66.96	597
HSA-MIR-4762-5P	99.57	68.54	1424
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-766-3P	99.47	65.24	1811

Cross-species orthologs

25 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf646	ENSDARG00000061424
danio_rerio	si:dkey-89b17.4	ENSDARG00000075545
danio_rerio	zgc:66472	ENSDARG00000075916
danio_rerio	si:ch211-148l7.4	ENSDARG00000094469
danio_rerio	znf576.1	ENSDARG00000097819
drosophila_melanogaster	Sry-delta	FBGN0003512
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	hang	FBGN0026575
drosophila_melanogaster	CG3032	FBGN0029928
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG11695	FBGN0030316
drosophila_melanogaster	CG8944	FBGN0030680
drosophila_melanogaster	CG7101	FBGN0030963
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	CG8089	FBGN0033993
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG10654	FBGN0036294
drosophila_melanogaster	CG6791	FBGN0037918
drosophila_melanogaster	CG17803	FBGN0038547
drosophila_melanogaster	CG12219	FBGN0043796
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	pzg	FBGN0259785
drosophila_melanogaster	mld	FBGN0263490
drosophila_melanogaster	zf30C	FBGN0270924
caenorhabditis_elegans		WBGENE00013734

Paralogs (36): ZNF302 (ENSG00000089335), ZNF184 (ENSG00000096654), CTCF (ENSG00000102974), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Zinc finger protein 497 — Q6ZNH5 (reviewed: Q6ZNH5)

All UniProt accessions (2): Q6ZNH5, M0R159

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 (2): NP_001193938, NP_940860* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096

UniProt features (21 total): zinc finger region 14, sequence conflict 4, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNH5-F1	78.74	0.46

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 31 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FOXJ2_TARGET_GENES, FOXN3_TARGET_GENES, HOXB4_TARGET_GENES, PITX1_TARGET_GENES, PPARGC1A_TARGET_GENES, MIR7106_5P, MIR4267, MIR6863, SAFB2_TARGET_GENES, MANNO_MIDBRAIN_NEUROTYPES_HRGL2A

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892)

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), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), 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
regulation of DNA-templated transcription	3
transcription by RNA polymerase II	1
DNA-templated transcription	1
negative regulation of RNA biosynthetic process	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
nucleic acid binding	1
binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

256 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF497	ARMH2	H3BNL8	580
ZNF497	RNF208	Q9H0X6	570
ZNF497	ZMYND12	Q9H0C1	479
ZNF497	ENTREP1	Q15884	476
ZNF497	PARP8	Q8N3A8	404
ZNF497	CCDC150	Q8NCX0	402
ZNF497	ZBED1	O96006	399
ZNF497	CCDC30	Q5VVM6	371
ZNF497	TCTN1	Q2MV58	368
ZNF497	TAFA2	Q8N3H0	327
ZNF497	S100A13	Q99584	317
ZNF497	HEXA	P06865	311
ZNF497	CATSPER3	Q86XQ3	307
ZNF497	TMEM132A	Q24JP5	301
ZNF497	CCNDBP1	O95273	287

IntAct

163 interactions, top by confidence:

A	B	Type	Score
ZNF497	CTSD	psi-mi:“MI:0915”(physical association)	0.610
CTSD	ZNF497	psi-mi:“MI:0915”(physical association)	0.610
NOTCH2NLC	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-2	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF792	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	PICK1	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.560
PTPN21	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	ZBTB8A	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	ZNF526	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	HOOK2	psi-mi:“MI:0915”(physical association)	0.560
KRTAP12-3	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	KRTAP4-4	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	ZNF473	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	GGA3	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
KHDRBS2	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
KRTAP1-3	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	TRIM41	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	PURB	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF837	ZNF497	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	MDFI	psi-mi:“MI:0915”(physical association)	0.560
ZNF497	OSBPL3	psi-mi:“MI:0915”(physical association)	0.560
MCC	ZNF497	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (46): ZNF497 (Two-hybrid), ZNF497 (Affinity Capture-MS), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid), ZNF497 (Two-hybrid)

ESM2 similar proteins: A6NFI3, A6NM28, A8K8V0, O75467, O95201, P10075, P10078, P10754, P28698, P30373, P52736, P70338, Q0VCC5, Q14929, Q16587, Q17QR7, Q3KNW1, Q3URR7, Q3US17, Q58DK7, Q5FWU5, Q5RJR4, Q5T619, Q5U4E2, Q68H95, Q6AW86, Q6PD29, Q6PGE4, Q6ZMY9, Q6ZNH5, Q7Z7K2, Q8BI73, Q8JZL0, Q8N393, Q8N8E2, Q8NCA9, Q8R0T2, Q96BV0, Q96C28, Q96H86

Diamond homologs: B0K011, B0X9H6, E9Q6W4, O75362, O77459, P28698, P31509, P60319, P80944, P86413, Q01798, Q02026, Q02027, Q08DS3, Q0IHB8, Q292R5, Q29419, Q32NK7, Q3T135, Q3US17, Q567J8, Q5SVQ8, Q5XJQ7, Q66JF8, Q6AY34, Q6ZNH5, Q811F1, Q8BX22, Q8BY46, Q8N2R0, Q8TAX0, Q8TBZ5, Q8WUU4, Q91ZD1, Q99PV8, Q9C0K0, Q9H165, Q9H4T2, Q9QX96, Q9QYE3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 51 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
Keratinization	9	15.2×	5e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	112
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

944 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58357647:GACCT:G	acceptor_loss	0.9900
19:58357651:T:G	acceptor_loss	0.9900
19:58358483:CCATA:C	donor_loss	0.9900
19:58358484:CATAC:C	donor_loss	0.9900
19:58358485:ATAC:A	donor_loss	0.9900
19:58358486:TA:T	donor_loss	0.9900
19:58358488:CC:C	donor_loss	0.9900
19:58358902:T:C	donor_gain	0.9900
19:58361944:T:TA	donor_gain	0.9900
19:58362428:A:C	donor_gain	0.9900
19:58362523:T:TA	donor_gain	0.9900
19:58358909:T:TA	donor_gain	0.9800
19:58358925:T:TA	donor_gain	0.9800
19:58362644:G:A	donor_gain	0.9800
19:58362675:ACCGT:A	donor_gain	0.9800
19:58362676:CCGTC:C	donor_gain	0.9800
19:58358585:CCT:C	acceptor_loss	0.9700
19:58358586:C:CA	acceptor_loss	0.9700
19:58358587:T:A	acceptor_loss	0.9700
19:58358901:A:AC	donor_gain	0.9700
19:58358919:G:C	donor_gain	0.9700
19:58358923:ACT:A	donor_gain	0.9700
19:58358924:CTC:C	donor_gain	0.9700
19:58358958:T:TA	donor_gain	0.9700
19:58362675:A:AC	donor_gain	0.9700
19:58362676:C:CC	donor_gain	0.9700
19:58357650:C:CC	acceptor_gain	0.9600
19:58357657:A:T	acceptor_gain	0.9600
19:58358901:AT:A	donor_gain	0.9600
19:58362481:T:TA	donor_gain	0.9600

AlphaMissense

3257 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:58357207:G:C	F143L	1.000
19:58357207:G:T	F143L	1.000
19:58357209:A:G	F143L	1.000
19:58356535:G:C	F367L	0.999
19:58356535:G:T	F367L	0.999
19:58356537:A:G	F367L	0.999
19:58356871:G:C	F255L	0.999
19:58356871:G:T	F255L	0.999
19:58356873:A:G	F255L	0.999
19:58356955:G:C	F227L	0.999
19:58356955:G:T	F227L	0.999
19:58356957:A:G	F227L	0.999
19:58357039:G:C	F199L	0.999
19:58357039:G:T	F199L	0.999
19:58357041:A:G	F199L	0.999
19:58357098:G:T	H180N	0.999
19:58357123:G:C	F171L	0.999
19:58357123:G:T	F171L	0.999
19:58357125:A:G	F171L	0.999
19:58357208:A:G	F143S	0.999
19:58357209:A:T	F143I	0.999
19:58356283:G:C	F451L	0.998
19:58356283:G:T	F451L	0.998
19:58356285:A:G	F451L	0.998
19:58356619:G:C	F339L	0.998
19:58356619:G:T	F339L	0.998
19:58356621:A:G	F339L	0.998
19:58356703:G:C	F311L	0.998
19:58356703:G:T	F311L	0.998
19:58356705:A:G	F311L	0.998

dbSNP variants (sampled 300 via entrez): RS1000283645 (19:58362062 T>C,G), RS1000479994 (19:58356961 C>G,T), RS1000962708 (19:58358154 CTCCACA>C), RS1001078658 (19:58357856 C>G,T), RS1001185552 (19:58357790 G>A,C,T), RS1001304020 (19:58362647 T>A), RS1001406924 (19:58359935 G>A), RS1001862443 (19:58363998 A>G), RS1001927471 (19:58360675 C>A), RS1001960006 (19:58361004 G>A), RS1002354462 (19:58362403 C>G), RS1002414843 (19:58362195 G>A,C), RS1002562361 (19:58356050 G>A,C), RS1002593331 (19:58358413 C>T), RS1002624385 (19:58358678 C>G,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

0 associations (top):

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
Tobacco Smoke Pollution	decreases expression, increases expression	2
Valproic Acid	decreases expression, increases methylation	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
propionaldehyde	decreases expression	1
kojic acid	decreases expression	1
butyraldehyde	decreases expression	1
ferrous chloride	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Glyphosate	decreases expression	1
Amiodarone	increases expression	1
Arbutin	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Triiodothyronine	increases expression	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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