ZNF628

Summary

ZNF628 (zinc finger protein 628, HGNC:28054) is a protein-coding gene on chromosome 19q13.42, encoding Zinc finger protein 628 (Q5EBL2). Transcriptional activator.

Zinc finger proteins (ZNFs), which bind nucleic acids, perform many key functions, the most important of which is regulating transcription. See ZNF91 (MIM 603971) for general information on ZNFs.

Source: NCBI Gene 89887 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 47 total
• MANE Select transcript: NM_033113

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28054
Approved symbol	ZNF628
Name	zinc finger protein 628
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	ZEC, Zfp628
Ensembl gene	ENSG00000197483
Ensembl biotype	protein_coding
OMIM	610671
Entrez	89887

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000591164, ENST00000598519

RefSeq mRNA: 1 — MANE Select: NM_033113 NM_033113

CCDS: CCDS33116

Canonical transcript exons

ENST00000598519 — 3 exons

Exon	Start	End
ENSE00001509550	55476617	55476807
ENSE00003543043	55479834	55479917
ENSE00003607687	55481201	55484487

Expression profiles

Bgee: expression breadth ubiquitous, 189 present calls, max score 92.18.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9131 / max 89.2489, expressed in 1748 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177619	7.8778	1729
177620	1.0352	694

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	92.18	gold quality
left testis	UBERON:0004533	82.34	gold quality
right testis	UBERON:0004534	82.02	gold quality
gastrocnemius	UBERON:0001388	80.96	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.86	gold quality
testis	UBERON:0000473	79.85	gold quality
muscle of leg	UBERON:0001383	78.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	78.17	gold quality
granulocyte	CL:0000094	77.48	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.03	silver quality
buccal mucosa cell	CL:0002336	76.33	silver quality
kidney epithelium	UBERON:0004819	75.94	gold quality
apex of heart	UBERON:0002098	75.29	gold quality
cerebellar vermis	UBERON:0004720	74.78	gold quality
mucosa of stomach	UBERON:0001199	74.43	gold quality
stromal cell of endometrium	CL:0002255	74.12	gold quality
lower esophagus muscularis layer	UBERON:0035833	74.07	gold quality
skin of abdomen	UBERON:0001416	74.05	gold quality
skin of leg	UBERON:0001511	74.05	gold quality
lower esophagus	UBERON:0013473	74.05	gold quality
muscle layer of sigmoid colon	UBERON:0035805	73.94	gold quality
pancreatic ductal cell	CL:0002079	73.76	silver quality
bone marrow cell	CL:0002092	73.76	gold quality
popliteal artery	UBERON:0002250	73.67	gold quality
leukocyte	CL:0000738	73.64	gold quality
tibial artery	UBERON:0007610	73.64	gold quality
monocyte	CL:0000576	73.46	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	73.46	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	73.43	gold quality
left uterine tube	UBERON:0001303	73.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

1 targeting ZNF628, 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-6889-5P	90.26	64.13	291

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp628	ENSMUSG00000074406
rattus_norvegicus	Zfp628	ENSRNOG00000038622

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), ZNF629 (ENSG00000102870), ZNF175 (ENSG00000105497), ZNF85 (ENSG00000105750), ZFP30 (ENSG00000120784), ZNF45 (ENSG00000124459), ZNF391 (ENSG00000124613), ZNF436 (ENSG00000125945), ZNF484 (ENSG00000127081), ZNF835 (ENSG00000127903), ZNF780B (ENSG00000128000), ZSCAN10 (ENSG00000130182), ZNF317 (ENSG00000130803), ZNF331 (ENSG00000130844), ZNF227 (ENSG00000131115), ZNF141 (ENSG00000131127), ZNF132 (ENSG00000131849), ZNF189 (ENSG00000136870), ZIM3 (ENSG00000141946), ZFP14 (ENSG00000142065), ZNF514 (ENSG00000144026), ZNF300 (ENSG00000145908), RBAK (ENSG00000146587), ZNF157 (ENSG00000147117), ZNF182 (ENSG00000147118), ZNF41 (ENSG00000147124), ZNF7 (ENSG00000147789), ZNF117 (ENSG00000152926), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631)

Protein

Protein identifiers

Zinc finger protein 628 — Q5EBL2 (reviewed: Q5EBL2)

All UniProt accessions (2): Q5EBL2, K7EL41

UniProt curated annotations — full annotation on UniProt →

Function. Transcriptional activator. Binds DNA on GT-box consensus sequence 5’-TTGGTT-3’. Plays a role in spermiogenesis.

Subunit / interactions. Interacts with TAF4B.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_149104* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (36 total): zinc finger region 16, region of interest 6, compositionally biased region 5, repeat 4, modified residue 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5EBL2-F1	58.39	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 (2): 199, 589

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GOBP_MALE_GAMETE_GENERATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MARTENS_TRETINOIN_RESPONSE_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, SRC_UP.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CREB3L4_TARGET_GENES, NCOA6_TARGET_GENES, NKX2_2_TARGET_GENES, ZNF592_TARGET_GENES, ZNF711_TARGET_GENES, ZNF92_TARGET_GENES, GSE8685_IL2_STARVED_VS_IL15_ACT_IL2_STARVED_CD4_TCELL_DN, GSE8685_IL2_STARVED_VS_IL21_ACT_IL2_STARVED_CD4_TCELL_DN

GO Biological Process (4): regulation of DNA-templated transcription (GO:0006355), spermatogenesis (GO:0007283), regulation of transcription by RNA polymerase II (GO:0006357), developmental process (GO:0032502)

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), zinc ion binding (GO:0008270), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515), 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	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
developmental process involved in reproduction	1
male gamete generation	1
transcription by RNA polymerase II	1
biological_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
transcription cis-regulatory region binding	1
transcription regulator activity	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

572 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF628	KIAA0408	Q6ZU52	576
ZNF628	TCEAL4	Q96EI5	559
ZNF628	FGD1	P98174	489
ZNF628	MIS18BP1	Q6P0N0	482
ZNF628	CAMTA2	O94983	456
ZNF628	CCDC80	Q76M96	447
ZNF628	INAFM1	C9JVW0	447
ZNF628	SAMD4A	Q9UPU9	443
ZNF628	ECSIT	Q9BQ95	431
ZNF628	ZBED6	P86452	424
ZNF628	SCAMP5	Q8TAC9	415
ZNF628	MSMB	P08118	382
ZNF628	UBALD1	Q8TB05	377
ZNF628	RUNDC1	Q96C34	371
ZNF628	GTF2A1	P52655	361

IntAct

21 interactions, top by confidence:

A	B	Type	Score
EXOC8	ZNF628	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF628	psi-mi:“MI:0915”(physical association)	0.560
ZNF628	MIEF2	psi-mi:“MI:0915”(physical association)	0.560
ZNF628	EXOC8	psi-mi:“MI:0915”(physical association)	0.560
EFEMP1	ZNF316	psi-mi:“MI:0914”(association)	0.350
SCRIB	C1orf226	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN2	ZNF316	psi-mi:“MI:0914”(association)	0.350
P4HA1	POLRMT	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350
GOLGA6L9	ZNF628	psi-mi:“MI:0915”(physical association)	0.000
ZNF628	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
MIEF2	ZNF628	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (22): ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-RNA), ZNF628 (Two-hybrid), ZNF628 (Two-hybrid), GOLGA6L9 (Two-hybrid), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-MS), ZNF628 (Affinity Capture-RNA), ZNF628 (Affinity Capture-MS)

ESM2 similar proteins: A2A5K6, A6QR00, D4A8X0, E9Q6W4, G3V893, O15015, O15156, O95863, P0CJ78, P10074, Q02085, Q13105, Q29RK0, Q3U3I9, Q4R8S8, Q504L7, Q5EBL2, Q5F293, Q5R4P8, Q5RJR4, Q60821, Q66K89, Q6DD87, Q6GL52, Q6NV66, Q6PGE4, Q6YND2, Q6ZN55, Q80VM4, Q8BI66, Q8BI69, Q8BIF9, Q8BY46, Q8CCE9, Q8CJ78, Q8JZL0, Q8N1W2, Q8NCA9, Q8TF50, Q8WUU4

Diamond homologs: O15090, O43167, P17041, P18732, P18744, P18747, Q5EBL2, Q62255, Q80X44, Q8CJ78, Q8K083, Q8TBZ5, Q96BV0, Q9BXA9, Q9ER74, Q9NSC2, Q9UDV7, O15391, P08045, P18712, P18731, P25490, P38621, Q00899, Q19A41, Q3TTC2, Q86T29, Q86UQ0, Q8BI66, Q8BIQ3, Q8BX22, Q8ST83, Q8TF50, Q96LX8, Q99PV8, Q9H165, Q9H4T2, Q9QYE3, Q9UJQ4, Q9VHJ6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

352 predictions. Top by Δscore:

Variant	Effect	Δscore
19:55477198:G:T	donor_gain	0.9700
19:55476803:CGCAG:C	donor_loss	0.9600
19:55476804:GCAGG:G	donor_loss	0.9600
19:55476805:CAG:C	donor_loss	0.9600
19:55476806:AG:A	donor_loss	0.9600
19:55476807:GGTG:G	donor_loss	0.9600
19:55476808:G:A	donor_loss	0.9600
19:55476809:T:G	donor_loss	0.9600
19:55481195:CCCCA:C	acceptor_loss	0.9500
19:55481196:CCCA:C	acceptor_loss	0.9500
19:55481197:CCA:C	acceptor_loss	0.9500
19:55481198:CAGG:C	acceptor_loss	0.9500
19:55481199:A:C	acceptor_loss	0.9500
19:55481200:G:T	acceptor_loss	0.9500
19:55481200:GGT:G	acceptor_gain	0.9500
19:55477243:G:T	donor_gain	0.9200
19:55481199:A:AG	acceptor_gain	0.9200
19:55481200:G:GG	acceptor_gain	0.9200
19:55477199:G:T	donor_gain	0.9000
19:55476679:G:GT	donor_gain	0.8900
19:55477243:G:GT	donor_gain	0.8700
19:55481188:ATCCC:A	acceptor_loss	0.8600
19:55481189:TCCCT:T	acceptor_loss	0.8600
19:55481190:CCCTC:C	acceptor_loss	0.8600
19:55481191:CCTCC:C	acceptor_loss	0.8600
19:55481192:CTCCC:C	acceptor_loss	0.8600
19:55476648:T:G	donor_gain	0.8500
19:55481187:AATCC:A	acceptor_loss	0.8500
19:55481193:TCCCC:T	acceptor_loss	0.8500
19:55481194:CCCCC:C	acceptor_loss	0.8500

AlphaMissense

6741 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:55481326:T:C	F45L	1.000
19:55481328:C:A	F45L	1.000
19:55481328:C:G	F45L	1.000
19:55481353:C:A	H54N	1.000
19:55481353:C:G	H54D	1.000
19:55481389:T:C	C66R	1.000
19:55481398:T:C	C69R	1.000
19:55481410:T:C	F73L	1.000
19:55481411:T:C	F73S	1.000
19:55481412:C:A	F73L	1.000
19:55481412:C:G	F73L	1.000
19:55481437:C:G	H82D	1.000
19:55481494:T:C	F101L	1.000
19:55481495:T:C	F101S	1.000
19:55481496:C:A	F101L	1.000
19:55481496:C:G	F101L	1.000
19:55481521:C:G	H110D	1.000
19:55481557:T:C	C122R	1.000
19:55481578:T:C	F129L	1.000
19:55481579:T:C	F129S	1.000
19:55481580:C:A	F129L	1.000
19:55481580:C:G	F129L	1.000
19:55481605:C:G	H138D	1.000
19:55481641:T:C	C150R	1.000
19:55481650:T:C	C153R	1.000
19:55481662:T:C	F157L	1.000
19:55481664:C:A	F157L	1.000
19:55481664:C:G	F157L	1.000
19:55481746:T:C	F185L	1.000
19:55481747:T:C	F185S	1.000

dbSNP variants (sampled 300 via entrez): RS1000040544 (19:55482939 G>A), RS1000057773 (19:55483437 C>T), RS1000306157 (19:55484954 C>G,T), RS1000432426 (19:55480162 G>T), RS1000934044 (19:55477017 C>T), RS1001275739 (19:55483753 G>A), RS1001284360 (19:55476721 C>A,T), RS1001890103 (19:55477494 G>A), RS1002272881 (19:55481119 C>G,T), RS1002282237 (19:55476600 C>T), RS1002629067 (19:55478338 G>A,C), RS1002774447 (19:55477353 G>T), RS1002935256 (19:55474900 A>C,G), RS1002946866 (19:55478568 C>G,T), RS1003293343 (19:55474696 A>C)

Disease associations

OMIM: gene MIM:610671 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST008362_35	Birth weight	2.000000e-09
GCST012227_1355	Hip circumference adjusted for BMI	2.000000e-10
GCST90000025_575	Appendicular lean mass	9.000000e-32
GCST90000026_17	Appendicular lean mass	3.000000e-22
GCST90000027_3	Appendicular lean mass	2.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004344	birth weight
EFO:0008039	BMI-adjusted hip circumference
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, decreases expression	3
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
fluorene-9-bisphenol	decreases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
ochratoxin A	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
licochalcone B	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Arsenic Trioxide	decreases expression	1
Hexachlorocyclohexane	decreases expression	1
Cisplatin	decreases expression	1
Diazinon	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, decreases expression	1
Propanil	decreases expression	1
Silicon Dioxide	decreases methylation	1
Smoke	increases expression	1
Thiram	increases expression	1
Urethane	affects expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases expression	1
Cadmium Chloride	decreases expression	1
Sirolimus	decreases expression	1

Clinical trials (associated diseases)

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