ZNF597

Summary

ZNF597 (zinc finger protein 597, HGNC:26573) is a protein-coding gene on chromosome 16p13.3, encoding Zinc finger protein 597 (Q96LX8). May be involved in transcriptional regulation.

This gene encodes a protein with multiple zinc finger domains. Loss of the related gene in rodents results in defects in neural development and embryonic lethality in mutant homozygotes. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and maternally expressed.

Source: NCBI Gene 146434 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_152457

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26573
Approved symbol	ZNF597
Name	zinc finger protein 597
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33071, HIT-4
Ensembl gene	ENSG00000167981
Ensembl biotype	protein_coding
OMIM	614685
Entrez	146434

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000301744

RefSeq mRNA: 1 — MANE Select: NM_152457 NM_152457

CCDS: CCDS10505

Canonical transcript exons

ENST00000301744 — 4 exons

Exon	Start	End
ENSE00001118946	3443121	3443206
ENSE00001118947	3440807	3440933
ENSE00001118948	3432414	3437538
ENSE00001118949	3443360	3443504

Expression profiles

Bgee: expression breadth ubiquitous, 178 present calls, max score 95.91.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9259 / max 75.2509, expressed in 1503 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156031	3.8142	1498
156032	0.1117	36

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	95.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.88	gold quality
oviduct epithelium	UBERON:0004804	76.30	gold quality
oocyte	CL:0000023	74.90	gold quality
epithelial cell of pancreas	CL:0000083	74.81	silver quality
buccal mucosa cell	CL:0002336	71.66	gold quality
visceral pleura	UBERON:0002401	71.34	gold quality
parietal pleura	UBERON:0002400	71.20	gold quality
germinal epithelium of ovary	UBERON:0001304	70.70	silver quality
granulocyte	CL:0000094	70.38	gold quality
stromal cell of endometrium	CL:0002255	70.22	gold quality
palpebral conjunctiva	UBERON:0001812	69.95	gold quality
islet of Langerhans	UBERON:0000006	69.90	gold quality
cortical plate	UBERON:0005343	69.68	gold quality
adrenal tissue	UBERON:0018303	69.28	gold quality
ventricular zone	UBERON:0003053	68.84	gold quality
leukocyte	CL:0000738	68.79	gold quality
monocyte	CL:0000576	68.42	gold quality
calcaneal tendon	UBERON:0003701	68.41	gold quality
cartilage tissue	UBERON:0002418	67.35	silver quality
gall bladder	UBERON:0002110	66.96	gold quality
left adrenal gland	UBERON:0001234	66.88	gold quality
smooth muscle tissue	UBERON:0001135	66.84	gold quality
prefrontal cortex	UBERON:0000451	66.73	gold quality
descending thoracic aorta	UBERON:0002345	66.59	gold quality
left adrenal gland cortex	UBERON:0035825	66.48	gold quality
right adrenal gland cortex	UBERON:0035827	66.48	gold quality
embryo	UBERON:0000922	66.43	gold quality
ganglionic eminence	UBERON:0004023	66.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

153 targeting ZNF597, 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-4262	100.00	73.26	3931
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-1277-5P	100.00	73.95	5056
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-450A-1-3P	100.00	69.33	1837
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3688-3P	99.97	72.02	2834

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	prdm2a	ENSDARG00000090721
mus_musculus	Zfp597	ENSMUSG00000039789
rattus_norvegicus	Zfp597	ENSRNOG00000088895
drosophila_melanogaster	CG12769	FBGN0033252
caenorhabditis_elegans		WBGENE00001223
caenorhabditis_elegans		WBGENE00017406
caenorhabditis_elegans		WBGENE00019960

Paralogs (7): ZNF423 (ENSG00000102935), ZNF211 (ENSG00000121417), ZNF462 (ENSG00000148143), ZBTB39 (ENSG00000166860), ZNF445 (ENSG00000185219), ZNF786 (ENSG00000197362), ZNF521 (ENSG00000198795)

Protein

Protein identifiers

Zinc finger protein 597 — Q96LX8 (reviewed: Q96LX8)

All UniProt accessions (1): Q96LX8

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Induction. Imprinted. Promoter methylation of the paternal allele may restrict expression to the maternal allele in leukocytes.

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

RefSeq proteins (1): NP_689670* (*=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 (11 total): zinc finger region 7, chain 1, domain 1, sequence variant 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96LX8-F1	48.97	0.00

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 (1): 300

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 92 (showing top): GGAANCGGAANY_UNKNOWN, PPAR_DR1_Q2, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, WARTERS_IR_RESPONSE_5GY, GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, MIR4262, MIR548P, MIR3121_3P, MIR106B_5P, MIR20A_5P, MIR181A_5P_MIR181B_5P

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), 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 (1): nucleus (GO:0005634)

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
transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
cis-regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	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

Protein interactions and networks

STRING

606 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF597	NAA60	Q9H7X0	723
ZNF597	ADNP	Q9H2P0	608
ZNF597	ZDBF2	Q9HCK1	587
ZNF597	FAM50B	Q9Y247	507
ZNF597	AASDHPPT	Q9NRN7	481
ZNF597	MEST	Q5EB52	447
ZNF597	USB1	Q9BQ65	433
ZNF597	GNAS	Q5JWF2	422
ZNF597	MCTS2	A0A3B3IRV3	398
ZNF597	HDGF	P51858	398
ZNF597	NAP1L5	Q96NT1	381
ZNF597	YBX1	P16990	377
ZNF597	ZC3H12C	Q9C0D7	370
ZNF597	CCDC185	Q8N715	360
ZNF597	SNRPN	P14648	353

IntAct

44 interactions, top by confidence:

A	B	Type	Score
ZNF597	TASOR2	psi-mi:“MI:0914”(association)	0.640
ZNF597	SYT17	psi-mi:“MI:0915”(physical association)	0.560
ZNF597	IRAK4	psi-mi:“MI:0915”(physical association)	0.560
ZNF597	CIB3	psi-mi:“MI:0915”(physical association)	0.560
CASP6	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
DMWD	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
LAMP2	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
LMNA	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
RAN	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
OPTN	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	ZNF597	psi-mi:“MI:0915”(physical association)	0.560
ZNF597	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
ZNF597	HCFC1	psi-mi:“MI:0914”(association)	0.530

BioGRID (44): ZNF597 (Two-hybrid), SMC6 (Affinity Capture-MS), NSMCE2 (Affinity Capture-MS), MPHOSPH8 (Affinity Capture-MS), NDNL2 (Affinity Capture-MS), SMC5 (Affinity Capture-MS), FAM208B (Affinity Capture-MS), NSMCE1 (Affinity Capture-MS), PPHLN1 (Affinity Capture-MS), NSMCE4A (Affinity Capture-MS), MPHOSPH8 (Affinity Capture-MS), SMC5 (Affinity Capture-MS), NSMCE2 (Affinity Capture-MS), FAM208B (Affinity Capture-MS), SMC6 (Affinity Capture-MS)

ESM2 similar proteins: A0JPL0, A1KXM5, A3CEM4, A6NK53, A7KBS4, A7MBI1, A8K554, A8MT65, A8MUZ8, A8MWA4, B1APH4, B2RXC5, E7ETH6, E9Q8G5, F4KIH4, G3X9G7, O14628, P0CH99, P0CI00, P18853, Q32L17, Q3MJ40, Q3URS2, Q49AA0, Q4V8E9, Q5EBM4, Q5FWF6, Q5RE50, Q5REN4, Q6V9R5, Q6ZN11, Q6ZN79, Q755V9, Q80VJ6, Q86TJ5, Q8BGV5, Q8N535, Q8N720, Q8N859, Q8NC26

Diamond homologs: O15391, P08045, P18712, P18731, P18732, P18747, P25490, P38621, Q00899, Q19A41, Q3TTC2, Q5EBL2, Q62255, Q86T29, Q86UQ0, Q8BI66, Q8BIQ3, Q8BX22, Q8CJ78, Q8ST83, Q8TBZ5, Q8TF50, Q96LX8, Q99PV8, Q9BXA9, Q9ER74, Q9H165, Q9H4T2, Q9NSC2, Q9QYE3, Q9UJQ4, Q9VHJ6, O15090, P98182, Q6NX45, Q8CF60, Q8K083, Q9NX65, Q9UL36, Q8N988

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

531 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3440802:CTTA:C	donor_loss	1.0000
16:3440804:TACC:T	donor_loss	1.0000
16:3440805:A:AC	donor_gain	1.0000
16:3440805:AC:A	donor_gain	1.0000
16:3440805:ACCCA:A	donor_loss	1.0000
16:3440806:C:CC	donor_gain	1.0000
16:3440806:CC:C	donor_gain	1.0000
16:3440806:CCCAT:C	donor_gain	1.0000
16:3440929:GGTCC:G	acceptor_gain	1.0000
16:3440931:TCC:T	acceptor_gain	1.0000
16:3440932:CC:C	acceptor_gain	1.0000
16:3440932:CCC:C	acceptor_gain	1.0000
16:3440933:CC:C	acceptor_gain	1.0000
16:3440933:CCT:C	acceptor_loss	1.0000
16:3440934:C:A	acceptor_loss	1.0000
16:3440934:C:CC	acceptor_gain	1.0000
16:3440935:T:G	acceptor_loss	1.0000
16:3443116:CTCA:C	donor_loss	1.0000
16:3443202:CAAAG:C	acceptor_gain	1.0000
16:3443203:AAAG:A	acceptor_gain	1.0000
16:3443204:AAG:A	acceptor_gain	1.0000
16:3443205:AG:A	acceptor_gain	1.0000
16:3443206:GCTG:G	acceptor_loss	1.0000
16:3443207:C:CC	acceptor_gain	1.0000
16:3443208:T:C	acceptor_loss	1.0000
16:3443354:ACTT:A	donor_loss	1.0000
16:3443355:CTTA:C	donor_loss	1.0000
16:3443358:A:AC	donor_gain	1.0000
16:3443359:C:CC	donor_gain	1.0000
16:3443359:C:CG	donor_loss	1.0000

AlphaMissense

2844 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:3437036:A:C	F221L	1.000
16:3437036:A:T	F221L	1.000
16:3437038:A:G	F221L	1.000
16:3436952:A:C	F249L	0.999
16:3436952:A:T	F249L	0.999
16:3436954:A:G	F249L	0.999
16:3437013:C:G	R229P	0.999
16:3437019:A:G	L227P	0.999
16:3437037:A:G	F221S	0.999
16:3437081:A:C	H206Q	0.999
16:3437081:A:T	H206Q	0.999
16:3437087:T:A	R204S	0.999
16:3437087:T:G	R204S	0.999
16:3437095:G:C	H202D	0.999
16:3437103:A:G	L199P	0.999
16:3437120:G:C	F193L	0.999
16:3437120:G:T	F193L	0.999
16:3437122:A:G	F193L	0.999
16:3437179:G:C	H174D	0.999
16:3437179:G:T	H174N	0.999
16:3437204:G:C	F165L	0.999
16:3437204:G:T	F165L	0.999
16:3437206:A:G	F165L	0.999
16:3436997:G:C	H234Q	0.998
16:3436997:G:T	H234Q	0.998
16:3437009:G:C	H230Q	0.998
16:3437009:G:T	H230Q	0.998
16:3437011:G:C	H230D	0.998
16:3437011:G:T	H230N	0.998
16:3437031:T:G	Q223P	0.998

dbSNP variants (sampled 300 via entrez): RS1000055627 (16:3443745 A>C), RS1000111807 (16:3444239 G>T), RS1000163608 (16:3440006 G>A,C), RS1000305342 (16:3440253 C>G), RS1000516334 (16:3441015 A>C), RS1000545509 (16:3441834 G>A,C), RS1000588466 (16:3441171 G>A,C), RS1000705420 (16:3438163 T>G), RS1001013482 (16:3437857 G>A), RS1001286985 (16:3444483 T>C), RS1001417976 (16:3440636 A>G), RS1001469987 (16:3440506 C>G,T), RS1001697270 (16:3444257 A>C), RS1001907957 (16:3431921 G>A), RS1001944160 (16:3435404 G>A)

Disease associations

OMIM: gene MIM:614685 | 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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases methylation, increases expression	2
Cisplatin	affects expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
2-methyl-4-isothiazolin-3-one	increases expression	1
terbufos	increases methylation	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
Temozolomide	increases expression	1
Decitabine	affects expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Estradiol	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Parathion	increases methylation	1
Valproic Acid	increases methylation	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Acrylamide	increases expression	1
Volatile Organic Compounds	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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