ZNF625

Summary

ZNF625 (zinc finger protein 625, HGNC:30571) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 625 (Q96I27). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription 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 90589 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 36 total
• MANE Select transcript: NM_145233

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30571
Approved symbol	ZNF625
Name	zinc finger protein 625
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000257591
Ensembl biotype	protein_coding
Entrez	90589

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000414892, ENST00000439556, ENST00000455799

RefSeq mRNA: 1 — MANE Select: NM_145233 NM_145233

CCDS: CCDS12269

Canonical transcript exons

ENST00000439556 — 4 exons

Exon	Start	End
ENSE00001628058	12144890	12146224
ENSE00002353231	12156556	12156734
ENSE00003467303	12147676	12147802
ENSE00003622438	12147395	12147455

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 86.07.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6641 / max 22.7727, expressed in 358 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179291	5.4830	1413
179290	0.4125	214
179292	0.2516	115

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	86.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.80	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.00	gold quality
ganglionic eminence	UBERON:0004023	81.63	gold quality
cortical plate	UBERON:0005343	77.23	gold quality
calcaneal tendon	UBERON:0003701	75.06	gold quality
adrenal tissue	UBERON:0018303	73.55	gold quality
stromal cell of endometrium	CL:0002255	72.83	gold quality
metanephros cortex	UBERON:0010533	70.22	gold quality
granulocyte	CL:0000094	69.78	gold quality
right hemisphere of cerebellum	UBERON:0014890	69.70	gold quality
islet of Langerhans	UBERON:0000006	69.68	gold quality
cerebellar cortex	UBERON:0002129	69.56	gold quality
cerebellar hemisphere	UBERON:0002245	69.49	gold quality
right lobe of thyroid gland	UBERON:0001119	69.42	gold quality
sural nerve	UBERON:0015488	69.38	gold quality
right adrenal gland cortex	UBERON:0035827	68.87	gold quality
left adrenal gland	UBERON:0001234	68.71	gold quality
left adrenal gland cortex	UBERON:0035825	68.58	gold quality
adenohypophysis	UBERON:0002196	68.51	gold quality
left lobe of thyroid gland	UBERON:0001120	68.38	gold quality
right adrenal gland	UBERON:0001233	68.18	gold quality
smooth muscle tissue	UBERON:0001135	68.14	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	68.11	gold quality
tendon	UBERON:0000043	68.08	gold quality
hypothalamus	UBERON:0001898	68.02	gold quality
cerebellum	UBERON:0002037	67.95	gold quality
thyroid gland	UBERON:0002046	67.78	gold quality
adrenal gland	UBERON:0002369	67.62	gold quality
descending thoracic aorta	UBERON:0002345	67.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.64

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting ZNF625, 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-150-5P	99.99	66.69	1976
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6815-3P	99.13	68.98	1530
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-606	98.72	67.34	960
HSA-MIR-619-5P	98.57	64.97	1988
HSA-MIR-4799-3P	97.78	65.97	893
HSA-MIR-4720-5P	97.46	65.67	893
HSA-MIR-5588-5P	97.46	65.70	913
HSA-MIR-134-5P	97.11	66.52	976
HSA-MIR-3118	97.11	66.58	984
HSA-MIR-450A-5P	93.89	64.57	50

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), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391)

Protein

Protein identifiers

Zinc finger protein 625 — Q96I27 (reviewed: Q96I27)

All UniProt accessions (3): Q96I27, F2Z3I2, H7C2C9

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?
Q96I27-1	1	yes
Q96I27-2	2

RefSeq proteins (1): NP_660276* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13912

UniProt features (14 total): zinc finger region 9, chain 1, region of interest 1, modified residue 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96I27-F1	76.26	0.52

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): 209

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 18 (showing top): GOZGIT_ESR1_TARGETS_DN, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF350_TARGET_GENES, ZNF513_TARGET_GENES, GSE11864_CSF1_IFNG_VS_CSF1_PAM3CYS_IN_MAC_DN, MIR6895_3P, SMN1_SMN2_TARGET_GENES, SCHERER_PBMC_APSV_WETVAX_AGE_18_32YO_50_TO_60DY_UP, GSE17974_0H_VS_0.5H_IN_VITRO_ACT_CD4_TCELL_UP, GSE17974_0H_VS_1H_IN_VITRO_ACT_CD4_TCELL_UP, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, GSE26928_NAIVE_VS_CXCR5_POS_CD4_TCELL_DN, GSE29614_CTRL_VS_TIV_FLU_VACCINE_PBMC_2007_DN

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

GO Molecular Function (6): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), 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
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

306 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF625	A0A087WYV9	A0A087WYV9	507
ZNF625	A0A0A6YYL1	A0A0A6YYL1	447
ZNF625	BEND5	Q7L4P6	397
ZNF625	MDFI	Q99750	348
ZNF625	CCDC180	Q9P1Z9	348
ZNF625	DMRTC2	Q8IXT2	347
ZNF625	ZGLP1	P0C6A0	334
ZNF625	AMER2	Q8N7J2	323
ZNF625	TMEM240	Q5SV17	322
ZNF625	LRRC31	Q6UY01	317
ZNF625	TAF6L	Q9Y6J9	306
ZNF625	GNA15	P30679	303
ZNF625	RUNDC3B	Q96NL0	293
ZNF625	MIER3	Q7Z3K6	278
ZNF625	ZNF385B	Q569K4	274

IntAct

19 interactions, top by confidence:

A	B	Type	Score
ZNF625	KRTAP10-4	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF625	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-9	ZNF625	psi-mi:“MI:0915”(physical association)	0.560
ZNF625	KRT40	psi-mi:“MI:0915”(physical association)	0.560
ZNF625		psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-4	ZNF625	psi-mi:“MI:0915”(physical association)	0.560
	ZNF625	psi-mi:“MI:0915”(physical association)	0.560
ZNF625	KRTAP10-9	psi-mi:“MI:0915”(physical association)	0.560
ECE1	ZNF625	psi-mi:“MI:0915”(physical association)	0.370
CBX5	ZNF568	psi-mi:“MI:0914”(association)	0.350
ZNF625	GGPS1	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): KRT40 (Two-hybrid), KRTAP10-4 (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-9 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZNF625 (Reconstituted Complex), ZNF625 (Two-hybrid), ZNF625 (Two-hybrid), ZNF625 (Proximity Label-MS), RRBP1 (Proximity Label-MS), KPRP (Affinity Capture-MS), GGPS1 (Affinity Capture-MS), ZNF625 (Affinity Capture-MS), ZNF625 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PQL4, A6NK53, A8MUZ8, A8MWA4, B1APH4, E7ETH6, O14628, O60384, P0CH99, P0CI00, P17024, P21506, P51502, P52741, P52743, P52744, Q0D2J5, Q13360, Q14593, Q15940, Q15973, Q4R882, Q5FWF6, Q5HY98, Q5JVG8, Q5RES8, Q6NX49, Q6P280, Q6V9R5, Q6ZN79, Q7L945, Q8BZW4, Q8IVC4, Q8IW36, Q8IZC7, Q8N587, Q8NDP4, Q8NE65, Q96H40, Q96I27

Diamond homologs: A0JPK3, A2RRD8, A2VDQ7, A3KN32, A8MUZ8, A8MWA4, C9JN71, E9QAG8, O60384, O60765, O75820, P0CH99, P0CI00, P10076, P10755, P15621, P16374, P16415, P17017, P17024, P51523, P52737, P52740, Q06730, Q06732, Q08AG5, Q0D2J5, Q13106, Q13360, Q15928, Q15935, Q15973, Q32M78, Q3KP31, Q4R4C7, Q4R6J4, Q4R882, Q5R9F0, Q5RC79, Q5REI6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	36
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

862 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12146223:CT:C	acceptor_gain	1.0000
19:12146225:C:CC	acceptor_gain	1.0000
19:12147671:CTTA:C	donor_loss	1.0000
19:12147672:TTA:T	donor_loss	1.0000
19:12147673:TACCT:T	donor_loss	1.0000
19:12147674:A:AC	donor_gain	1.0000
19:12147675:C:CC	donor_gain	1.0000
19:12147675:C:CT	donor_loss	1.0000
19:12147675:CCTA:C	donor_gain	1.0000
19:12147801:TC:T	acceptor_gain	1.0000
19:12147802:CC:C	acceptor_gain	1.0000
19:12147813:CCACA:C	acceptor_gain	1.0000
19:12147814:C:CT	acceptor_gain	1.0000
19:12147814:C:T	acceptor_gain	1.0000
19:12147814:CACA:C	acceptor_gain	1.0000
19:12147816:CA:C	acceptor_gain	1.0000
19:12147817:A:C	acceptor_gain	1.0000
19:12147819:G:C	acceptor_gain	1.0000
19:12156553:CAC:C	donor_loss	1.0000
19:12156554:A:AC	donor_gain	1.0000
19:12156554:AC:A	donor_gain	1.0000
19:12156554:ACCA:A	donor_loss	1.0000
19:12156554:ACCAT:A	donor_loss	1.0000
19:12156555:C:A	donor_loss	1.0000
19:12156555:C:CC	donor_gain	1.0000
19:12156555:CC:C	donor_gain	1.0000
19:12156555:CCA:C	donor_gain	1.0000
19:12146220:GACCT:G	acceptor_gain	0.9900
19:12146221:ACCTC:A	acceptor_loss	0.9900
19:12146224:TCTGT:T	acceptor_loss	0.9900

AlphaMissense

2472 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000235145 (19:12155969 GC>G,GCC), RS1000247500 (19:12150132 A>G,T), RS1000319240 (19:12149762 G>A), RS1000548840 (19:12147508 G>A), RS1000700716 (19:12154454 G>A), RS1000757280 (19:12154087 G>A), RS1000837389 (19:12154212 C>T), RS1001211295 (19:12150902 G>A), RS1001263635 (19:12150550 C>T), RS1001591273 (19:12149228 T>C), RS1001737016 (19:12155160 A>C), RS1001772156 (19:12157294 C>T), RS1002213567 (19:12149239 C>G,T), RS1002267696 (19:12148873 C>G,T), RS1002367101 (19:12156067 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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
butyraldehyde	increases expression	1
cupric oxide	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
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
Leflunomide	increases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation, decreases methylation	1
Folic Acid	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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