ZNF629

Summary

ZNF629 (zinc finger protein 629, HGNC:29008) is a protein-coding gene on chromosome 16p11.2, encoding Zinc finger protein 629 (Q9UEG4). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 23361 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 105 total
• MANE Select transcript: NM_001080417

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29008
Approved symbol	ZNF629
Name	zinc finger protein 629
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0326
Ensembl gene	ENSG00000102870
Ensembl biotype	protein_coding
OMIM	619587
Entrez	23361

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000262525, ENST00000896341

RefSeq mRNA: 2 — MANE Select: NM_001080417 NM_001080417, NM_001345970

CCDS: CCDS45463

Canonical transcript exons

ENST00000262525 — 3 exons

Exon	Start	End
ENSE00000682597	30778456	30784254
ENSE00000682598	30784410	30784515
ENSE00000682606	30787028	30787205

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 92.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.1289 / max 73.4863, expressed in 1743 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157092	13.7652	1743
157091	0.3637	179

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
type B pancreatic cell	CL:0000169	92.10	gold quality
olfactory bulb	UBERON:0002264	91.97	gold quality
diaphragm	UBERON:0001103	89.77	silver quality
tendon of biceps brachii	UBERON:0008188	87.40	gold quality
apex of heart	UBERON:0002098	85.58	gold quality
endometrium epithelium	UBERON:0004811	85.16	gold quality
paraflocculus	UBERON:0005351	84.52	gold quality
nasal cavity epithelium	UBERON:0005384	84.47	gold quality
cortical plate	UBERON:0005343	83.96	gold quality
tibialis anterior	UBERON:0001385	83.53	silver quality
left ventricle myocardium	UBERON:0006566	83.48	silver quality
endothelial cell	CL:0000115	83.39	silver quality
ganglionic eminence	UBERON:0004023	82.73	gold quality
lateral nuclear group of thalamus	UBERON:0002736	82.65	gold quality
heart left ventricle	UBERON:0002084	82.61	gold quality
cardiac ventricle	UBERON:0002082	82.56	gold quality
heart right ventricle	UBERON:0002080	82.45	gold quality
middle frontal gyrus	UBERON:0002702	82.41	gold quality
cardiac muscle of right atrium	UBERON:0003379	82.30	gold quality
ventricular zone	UBERON:0003053	82.26	gold quality
inferior olivary complex	UBERON:0002127	81.99	gold quality
frontal pole	UBERON:0002795	81.94	gold quality
embryo	UBERON:0000922	81.57	gold quality
stromal cell of endometrium	CL:0002255	81.44	gold quality
medial globus pallidus	UBERON:0002477	81.41	gold quality
quadriceps femoris	UBERON:0001377	81.36	silver quality
Brodmann (1909) area 10	UBERON:0013541	81.20	gold quality
CA1 field of hippocampus	UBERON:0003881	80.85	silver quality
deltoid	UBERON:0001476	80.83	silver quality
heart	UBERON:0000948	80.63	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	258.96
E-ANND-3	no	3.09

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp629	ENSMUSG00000045639
rattus_norvegicus	Zfp629	ENSRNOG00000018877

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), ZNF506 (ENSG00000081665), ZNF268 (ENSG00000090612), MZF1 (ENSG00000099326), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 629 — Q9UEG4 (reviewed: Q9UEG4)

Alternative names: Zinc finger protein 65

All UniProt accessions (1): Q9UEG4

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_001073886, NP_001332899 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096

UniProt features (34 total): zinc finger region 19, compositionally biased region 4, cross-link 4, region of interest 3, modified residue 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UEG4-F1	64.33	0.13

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 (6): 18, 616, 251, 688, 750, 840

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): KOYAMA_SEMA3B_TARGETS_UP, chr16p11, HAMAI_APOPTOSIS_VIA_TRAIL_DN, SAFFORD_T_LYMPHOCYTE_ANERGY, SENESE_HDAC3_TARGETS_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN, MARTENS_TRETINOIN_RESPONSE_DN, LU_EZH2_TARGETS_UP, KRIEG_HYPOXIA_NOT_VIA_KDM3A, IL2_UP.V1_DN, IL21_UP.V1_DN, DIDO1_TARGET_GENES, FOXD2_TARGET_GENES

GO Biological Process (1): regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), 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	1
transcription by RNA polymerase II	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2092 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF629	TRIM28	Q13263	981
ZNF629	ZUP1	Q96AP4	856
ZNF629	USP5	P45974	819
ZNF629	UBB	P02248	811
ZNF629	YOD1	Q5VVQ6	788
ZNF629	USP44	Q9H0E7	773
ZNF629	OTUD7A	Q8TE49	740
ZNF629	SETDB1	Q15047	673
ZNF629	ZPR1	O75312	670
ZNF629	CRBN	Q96SW2	663
ZNF629	HDAC6	Q9UBN7	653
ZNF629	UBA2	Q9UBT2	647
ZNF629	PHF20	Q9BVI0	638
ZNF629	NPLOC4	Q8TAT6	568
ZNF629	ZFAND5	O76080	558

IntAct

155 interactions, top by confidence:

A	B	Type	Score
YWHAB	PIK3C2A	psi-mi:“MI:0914”(association)	0.800
GTF3C3	POLR3D	psi-mi:“MI:0914”(association)	0.640
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
IPO8	TRIM28	psi-mi:“MI:0914”(association)	0.640
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
YWHAE	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAZ	PIK3C2A	psi-mi:“MI:0914”(association)	0.570
ZNF629	YJU2B	psi-mi:“MI:0915”(physical association)	0.560
ZNF629	TEPSIN	psi-mi:“MI:0915”(physical association)	0.560
ZNF629	PPP1CC	psi-mi:“MI:0915”(physical association)	0.560
	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
CCHCR1	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
CDR2L	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
HNF4G	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
ZNF629	ZRANB1	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
GAS8	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
LDOC1	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
TRIM41	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
ZNF438	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
JRK	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
SMARCD1	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
SPG21	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
ZNF629	RSPH14	psi-mi:“MI:0915”(physical association)	0.560
ZNF629	ISY1	psi-mi:“MI:0915”(physical association)	0.560
TEPSIN	ZNF629	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF629	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (141): ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Proximity Label-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-MS), ZNF629 (Affinity Capture-RNA)

ESM2 similar proteins: A1YEV9, A1YG26, A1YG48, A1YG60, A2T712, A2T736, A2T7D2, A2T7L7, A6QPT6, B2KFW1, O14771, O14978, O95125, P10073, P17029, P17040, P59923, Q07231, Q15776, Q16587, Q1LZ87, Q3URR7, Q4KLI1, Q4R8H9, Q53GI3, Q5R670, Q5R741, Q5RJ54, Q5VV52, Q63HK3, Q6A085, Q86W11, Q8BGS3, Q8CF60, Q8IWY8, Q8N393, Q8NF99, Q91VW9, Q969J2, Q96GC6

Diamond homologs: B1H2Q6, G5EGB2, O15535, O75290, P17026, P18724, P18741, P18747, P52742, Q15937, Q17895, Q1LZC0, Q3MJ62, Q4R7X8, Q5R4X5, Q6A085, Q7Z3I7, Q8BGV5, Q8TBZ5, Q91VW9, Q969J2, Q9BRR0, Q9ERU2, Q9ERU3, Q9UEG4, Q9Z1D9, Q9Z2K3, P18715, P18719, P18725, P18729, P18731, P18735, P18737, Q3TDE8, Q966L8, P18714, P18718, P18738, P18740

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 128 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
Activation of BAD and translocation to mitochondria	7	62.0×	2e-10
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	54.7×	4e-10
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	54.7×	4e-10
Activation of BH3-only proteins	7	40.4×	4e-09
SARS-CoV-1-host interactions	13	26.6×	3e-13
RHO GTPases activate PKNs	7	25.8×	1e-07
Intrinsic Pathway for Apoptosis	7	23.8×	2e-07
SARS-CoV-1 Infection	13	21.6×	9e-13

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	14	22.0×	1e-12
protein targeting	5	15.5×	2e-03
ribosomal small subunit biogenesis	8	15.4×	1e-05
translation	15	13.1×	2e-10
negative regulation of translation	6	10.0×	3e-03
rRNA processing	7	8.4×	2e-03
intracellular protein localization	8	7.1×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	94
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

650 predictions. Top by Δscore:

Variant	Effect	Δscore
16:30784255:CT:C	acceptor_loss	1.0000
16:30784514:CC:C	acceptor_gain	1.0000
16:30784515:CC:C	acceptor_gain	1.0000
16:30784516:C:CA	acceptor_loss	1.0000
16:30787027:CGG:C	donor_gain	1.0000
16:30787027:CGGCT:C	donor_gain	1.0000
16:30787080:AAC:A	donor_gain	1.0000
16:30787080:AACC:A	donor_gain	1.0000
16:30787081:A:C	donor_gain	1.0000
16:30784252:CAC:C	acceptor_gain	0.9900
16:30784255:C:CC	acceptor_gain	0.9900
16:30784404:CCTCA:C	donor_loss	0.9900
16:30784405:CTCAC:C	donor_loss	0.9900
16:30784406:TCA:T	donor_loss	0.9900
16:30784407:CACCT:C	donor_loss	0.9900
16:30784408:A:T	donor_loss	0.9900
16:30784409:C:CA	donor_loss	0.9900
16:30784409:CCT:C	donor_gain	0.9900
16:30784511:GGACC:G	acceptor_gain	0.9900
16:30784512:GACC:G	acceptor_gain	0.9900
16:30784513:ACC:A	acceptor_gain	0.9900
16:30784514:CCC:C	acceptor_gain	0.9900
16:30784516:C:CC	acceptor_gain	0.9900
16:30784516:C:T	acceptor_gain	0.9900
16:30787021:AACTC:A	donor_loss	0.9900
16:30787022:ACTC:A	donor_loss	0.9900
16:30787024:TCA:T	donor_loss	0.9900
16:30787025:CA:C	donor_loss	0.9900
16:30787026:A:AC	donor_gain	0.9900
16:30787026:AC:A	donor_loss	0.9900

AlphaMissense

5757 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:30782826:A:G	L501P	1.000
16:30782843:G:C	F495L	1.000
16:30782843:G:T	F495L	1.000
16:30782845:A:G	F495L	1.000
16:30782927:G:C	F467L	1.000
16:30782927:G:T	F467L	1.000
16:30782929:A:G	F467L	1.000
16:30782982:T:G	Q449P	1.000
16:30782984:G:C	H448Q	1.000
16:30782984:G:T	H448Q	1.000
16:30782986:G:C	H448D	1.000
16:30782986:G:T	H448N	1.000
16:30782994:A:G	L445P	1.000
16:30783011:G:C	F439L	1.000
16:30783011:G:T	F439L	1.000
16:30783012:A:G	F439S	1.000
16:30783013:A:G	F439L	1.000
16:30783034:A:G	C432R	1.000
16:30783070:G:C	H420D	1.000
16:30783078:A:G	L417P	1.000
16:30783095:G:C	F411L	1.000
16:30783095:G:T	F411L	1.000
16:30783097:A:G	F411L	1.000
16:30783118:A:G	C404R	1.000
16:30783246:A:G	L361P	1.000
16:30783263:G:C	F355L	1.000
16:30783263:G:T	F355L	1.000
16:30783265:A:G	F355L	1.000
16:30783308:G:C	H340Q	1.000
16:30783308:G:T	H340Q	1.000

dbSNP variants (sampled 300 via entrez): RS1000152871 (16:30778930 T>A,C), RS1000387459 (16:30786774 G>A,C), RS1000611485 (16:30783891 G>A), RS1001054900 (16:30785957 G>A,C), RS1001081345 (16:30782609 C>A,T), RS1001404331 (16:30785490 C>T), RS1001680733 (16:30787870 A>G), RS1001998718 (16:30784037 C>T), RS1002277226 (16:30786404 G>A), RS1002295598 (16:30778202 C>A,T), RS1002347886 (16:30778551 C>A,G,T), RS1002591817 (16:30786091 A>G), RS1003053732 (16:30786229 C>G,T), RS1003055532 (16:30781436 G>A), RS1003117998 (16:30778534 T>C)

Disease associations

OMIM: gene MIM:619587 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST011956_150	Systemic lupus erythematosus	3.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
Valproic Acid	decreases expression, increases methylation	2
Cyclosporine	decreases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
FR900359	decreases phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
benzo(e)pyrene	increases methylation	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Leflunomide	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Lead	affects expression	1
Methapyrilene	increases methylation	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Zidovudine	affects cotreatment, increases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_XW70	HEK293 eGFP-ZNF629	Transformed cell line	Female

Clinical trials (associated diseases)

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