ZNF610

Summary

ZNF610 (zinc finger protein 610, HGNC:26687) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 610 (Q8N9Z0). 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 162963 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_001161425

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26687
Approved symbol	ZNF610
Name	zinc finger protein 610
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	FLJ36040
Ensembl gene	ENSG00000167554
Ensembl biotype	protein_coding
Entrez	162963

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 retained_intron

ENST00000321287, ENST00000327920, ENST00000403906, ENST00000593698, ENST00000594919, ENST00000599508, ENST00000601151, ENST00000613461, ENST00000616431, ENST00000927695

RefSeq mRNA: 4 — MANE Select: NM_001161425 NM_001161425, NM_001161426, NM_001161427, NM_173530

CCDS: CCDS12851, CCDS54309

Canonical transcript exons

ENST00000403906 — 6 exons

Exon	Start	End
ENSE00001509748	52347707	52347944
ENSE00002470175	52349154	52349235
ENSE00002486704	52353682	52353808
ENSE00002504046	52354251	52354379
ENSE00002976700	52365698	52367778
ENSE00003081720	52336243	52336506

Expression profiles

Bgee: expression breadth ubiquitous, 190 present calls, max score 91.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.9761 / max 47.3264, expressed in 1099 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177299	2.2504	968
177298	0.6283	376
177301	0.0827	24
177300	0.0148	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	91.68	gold quality
secondary oocyte	CL:0000655	88.52	gold quality
ventricular zone	UBERON:0003053	86.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.03	gold quality
ganglionic eminence	UBERON:0004023	85.68	gold quality
cortical plate	UBERON:0005343	84.69	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.20	gold quality
right testis	UBERON:0004534	78.53	gold quality
pancreatic ductal cell	CL:0002079	77.58	silver quality
testis	UBERON:0000473	77.55	gold quality
left testis	UBERON:0004533	77.42	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	74.95	gold quality
prefrontal cortex	UBERON:0000451	74.37	gold quality
left ovary	UBERON:0002119	74.11	gold quality
right uterine tube	UBERON:0001302	73.93	gold quality
stromal cell of endometrium	CL:0002255	73.83	gold quality
caudate nucleus	UBERON:0001873	73.73	gold quality
spinal cord	UBERON:0002240	73.52	gold quality
sperm	CL:0000019	73.30	gold quality
gall bladder	UBERON:0002110	73.19	gold quality
tibialis anterior	UBERON:0001385	73.16	silver quality
smooth muscle tissue	UBERON:0001135	73.04	gold quality
ovary	UBERON:0000992	72.79	gold quality
putamen	UBERON:0001874	72.69	gold quality
nucleus accumbens	UBERON:0001882	72.62	gold quality
hypothalamus	UBERON:0001898	72.36	gold quality
right ovary	UBERON:0002118	72.17	gold quality
adrenal tissue	UBERON:0018303	72.14	gold quality
islet of Langerhans	UBERON:0000006	72.10	gold quality
right adrenal gland	UBERON:0001233	71.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-100618	no	92.39
E-ANND-3	no	4.74

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1713.1	ZNF610	More than 3 adjacent zinc fingers
MA1713.2	ZNF610	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28273063

miRNA regulators (miRDB)

26 targeting ZNF610, 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-3064-3P	100.00	70.09	1254
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-3911	99.38	66.95	1087
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-6792-3P	98.41	66.86	1359
HSA-MIR-10397-3P	97.78	65.70	601
HSA-MIR-4765	93.11	66.17	737

Literature-anchored findings (GeneRIF, showing 1)

• Silencing of ZNF610 suppresses cell proliferation and migration in lung adenocarcinoma. (PMID:38898665)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfx	ENSDARG00000074453
danio_rerio		ENSDARG00000098424
mus_musculus	Zfy2	ENSMUSG00000000103
mus_musculus	Zfy1	ENSMUSG00000053211
rattus_norvegicus	Zfy1	ENSRNOG00000053042

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 610 — Q8N9Z0 (reviewed: Q8N9Z0)

All UniProt accessions (2): Q8N9Z0, M0QYM6

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N9Z0-1	1	yes
Q8N9Z0-2	2

RefSeq proteins (4): NP_001154897, NP_001154898, NP_001154899, NP_775801 (=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, PF13465

UniProt features (19 total): zinc finger region 9, sequence variant 4, cross-link 3, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9Z0-F1	65.82	0.26

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 (3): 119, 122, 194

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway
R-HSA-9843940	Regulation of endogenous retroelements by KRAB-ZFP proteins

MSigDB gene sets: 27 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF528_TARGET_GENES, MIR4753_3P, MIR551B_5P, MIR6873_3P, MIR3064_3P, WRNIP1_TARGET_GENES, HARALAMBIEVA_PBMC_FLUARIX_AGE_50_74YO_CORR_WITH_28D_MEM_B_CELL_RESPONSE_AT_3DY_NEGATIVE, GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_18H_DN

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

GO Molecular Function (5): 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), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
RNA Polymerase II Transcription	1
Regulation of endogenous retroelements	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

330 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF610	OPLAH	O14841	417
ZNF610	FAM135B	Q49AJ0	411
ZNF610	TSPYL5	Q86VY4	399
ZNF610	ZC2HC1A	Q96GY0	377
ZNF610	ARHGEF4	Q9NR80	370
ZNF610	LRRC26	Q2I0M4	323
ZNF610	TBX15	Q96SF7	322
ZNF610	GIMAP6	Q6P9H5	307
ZNF610	DMRTA2	Q96SC8	304
ZNF610	VWC2	Q2TAL6	301
ZNF610	GRIN2D	O15399	280
ZNF610	RSPO2	Q6UXX9	276
ZNF610	MIA2	Q96PC5	272
ZNF610	PCDH10	Q9P2E7	270
ZNF610	EMX1	Q04741	254
ZNF610	SORCS3	Q9UPU3	254

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF610	CDC37	psi-mi:“MI:0915”(physical association)	0.400
ZNF610	TRIM37	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): TRIM37 (Affinity Capture-MS), TUBA3C (Affinity Capture-MS), HERC1 (Affinity Capture-MS), ZNF610 (Affinity Capture-MS), PLEKHA1 (Affinity Capture-MS), TRIM37 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), TUBA3C (Affinity Capture-MS), ZNF610 (Affinity Capture-MS), ZNF610 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	67
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1162 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52349066:GAT:G	donor_gain	1.0000
19:52349150:TTAG:T	acceptor_loss	1.0000
19:52349151:TAGG:T	acceptor_loss	1.0000
19:52349152:A:AT	acceptor_loss	1.0000
19:52349153:GGATT:G	acceptor_gain	1.0000
19:52353680:A:G	acceptor_loss	1.0000
19:52353680:AG:A	acceptor_gain	1.0000
19:52353681:GG:G	acceptor_gain	1.0000
19:52353681:GGGAC:G	acceptor_gain	1.0000
19:52365692:TTCTA:T	acceptor_loss	1.0000
19:52365693:TCTA:T	acceptor_loss	1.0000
19:52365694:CTA:C	acceptor_loss	1.0000
19:52365695:TAG:T	acceptor_loss	1.0000
19:52365696:AGGG:A	acceptor_loss	1.0000
19:52365697:G:A	acceptor_loss	1.0000
19:52347208:G:GT	donor_gain	0.9900
19:52347244:GCC:G	donor_gain	0.9900
19:52349152:A:AG	acceptor_gain	0.9900
19:52349153:G:GG	acceptor_gain	0.9900
19:52349231:CTCAG:C	donor_loss	0.9900
19:52349232:TCAG:T	donor_loss	0.9900
19:52349233:CAGGT:C	donor_loss	0.9900
19:52349234:AGGT:A	donor_loss	0.9900
19:52349235:GGT:G	donor_loss	0.9900
19:52349236:G:A	donor_loss	0.9900
19:52349237:T:A	donor_loss	0.9900
19:52353675:A:AG	acceptor_gain	0.9900
19:52353676:TTTTA:T	acceptor_gain	0.9900
19:52353677:TTTAG:T	acceptor_gain	0.9900
19:52353680:A:AG	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000049927 (19:52351929 C>G), RS1000140129 (19:52362925 A>C,G), RS1000148420 (19:52356490 T>C), RS1000232582 (19:52342451 A>G), RS1000280489 (19:52341240 T>C), RS1000388452 (19:52346911 G>C), RS1000405776 (19:52352380 A>G), RS1000617554 (19:52342581 G>A), RS1000730326 (19:52342302 A>G), RS1000931457 (19:52362993 G>A), RS1000993518 (19:52362796 T>G), RS1001118931 (19:52332116 G>C), RS1001164667 (19:52341502 G>A), RS1001281003 (19:52357286 G>T), RS1001301146 (19:52339386 A>C,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

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
Valproic Acid	affects expression, decreases expression, increases expression	4
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
bisphenol A	decreases expression	1
trichostatin A	increases expression	1
arsenite	increases reaction, affects binding	1
sodium arsenite	decreases expression	1
butylbenzyl phthalate	increases expression	1
nickel sulfate	decreases expression	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation, increases methylation	1
Cadmium	increases abundance, increases expression	1
Estradiol	affects expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_HD33	HEK293 eGFP-ZNF610	Transformed cell line	Female

Clinical trials (associated diseases)

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