ZNF302

Summary

ZNF302 (zinc finger protein 302, HGNC:13848) is a protein-coding gene on chromosome 19q13.11, encoding Zinc finger protein 302 (Q9NR11). May be involved in transcriptional regulation.

This gene encodes a member of the zinc-finger protein family. The encoded protein contains seven C2H2-type zinc fingers and a KRAB domain, but its function has yet to be determined. Alternatively spliced transcript variants have been described.

Source: NCBI Gene 55900 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 77 total
• MANE Select transcript: NM_001289187

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13848
Approved symbol	ZNF302
Name	zinc finger protein 302
Location	19q13.11
Locus type	gene with protein product
Status	Approved
Aliases	ZNF327, ZNF135L, ZNF140L
Ensembl gene	ENSG00000089335
Ensembl biotype	protein_coding
OMIM	621271
Entrez	55900

Gene structure

Transcript identifiers

Ensembl transcripts: 55 — 52 protein_coding, 3 retained_intron

ENST00000423823, ENST00000446502, ENST00000457781, ENST00000502743, ENST00000505163, ENST00000505242, ENST00000505365, ENST00000506901, ENST00000507959, ENST00000509196, ENST00000509528, ENST00000510002, ENST00000512455, ENST00000613363, ENST00000869116, ENST00000869117, ENST00000869118, ENST00000869119, ENST00000869120, ENST00000869121, ENST00000869122, ENST00000869123, ENST00000869124, ENST00000869125, ENST00000869126, ENST00000869127, ENST00000869128, ENST00000869129, ENST00000869130, ENST00000929232, ENST00000929233, ENST00000929234, ENST00000929235, ENST00000929236, ENST00000929237, ENST00000929238, ENST00000929239, ENST00000929240, ENST00000958495, ENST00000958496, ENST00000958497, ENST00000958498, ENST00000958499, ENST00000958500, ENST00000958501, ENST00000958502, ENST00000958503, ENST00000958504, ENST00000958505, ENST00000958506, ENST00000958507, ENST00000958508, ENST00000958509, ENST00000958510, ENST00000958511

RefSeq mRNA: 15 — MANE Select: NM_001289187 NM_001012320, NM_001289181, NM_001289182, NM_001289183, NM_001289184, NM_001289185, NM_001289186, NM_001289187, NM_001289188, NM_001289189, NM_001289190, NM_001289191, NM_001289192, NM_018443, NM_018675

CCDS: CCDS46042, CCDS74330, CCDS74331, CCDS74332, CCDS74333

Canonical transcript exons

ENST00000505242 — 5 exons

Exon	Start	End
ENSE00002032461	34677678	34678103
ENSE00002033950	34684252	34686396
ENSE00002492730	34682777	34682897
ENSE00003637046	34683155	34683238
ENSE00003709405	34678737	34678813

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 97.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.4253 / max 373.1940, expressed in 1709 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175150	13.8531	1694
175151	1.9444	1006
175149	0.6278	290

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.55	gold quality
sural nerve	UBERON:0015488	97.32	gold quality
buccal mucosa cell	CL:0002336	97.28	gold quality
cortical plate	UBERON:0005343	95.91	gold quality
calcaneal tendon	UBERON:0003701	95.19	gold quality
ganglionic eminence	UBERON:0004023	94.50	gold quality
germinal epithelium of ovary	UBERON:0001304	94.46	gold quality
cerebellar cortex	UBERON:0002129	94.21	gold quality
cerebellar hemisphere	UBERON:0002245	94.21	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.90	gold quality
biceps brachii	UBERON:0001507	93.77	gold quality
cerebellum	UBERON:0002037	93.60	gold quality
body of pancreas	UBERON:0001150	93.43	gold quality
ventricular zone	UBERON:0003053	93.03	gold quality
left ovary	UBERON:0002119	92.99	gold quality
right ovary	UBERON:0002118	92.76	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	92.67	gold quality
primary visual cortex	UBERON:0002436	92.62	gold quality
right uterine tube	UBERON:0001302	92.52	gold quality
gastrocnemius	UBERON:0001388	92.52	gold quality
muscle of leg	UBERON:0001383	92.24	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.22	gold quality
ovary	UBERON:0000992	92.15	gold quality
left lobe of thyroid gland	UBERON:0001120	92.11	gold quality
body of uterus	UBERON:0009853	92.11	gold quality
thyroid gland	UBERON:0002046	91.97	gold quality
right lobe of thyroid gland	UBERON:0001119	91.91	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.91	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.90	gold quality
lower esophagus muscularis layer	UBERON:0035833	91.76	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	10.90
E-ANND-3	yes	6.74
E-HCAD-31	no	828.89

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

75 targeting ZNF302, 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-3925-3P	100.00	69.95	1237
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
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-4262	100.00	73.26	3931
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-380-3P	99.89	70.18	1978
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832

Cross-species orthologs

16 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf646	ENSDARG00000061424
danio_rerio	si:dkey-154p10.3	ENSDARG00000068366
danio_rerio	si:dkey-89b17.4	ENSDARG00000075545
danio_rerio	zgc:66472	ENSDARG00000075916
danio_rerio	si:ch211-148l7.4	ENSDARG00000094469
danio_rerio	znf576.1	ENSDARG00000097819
drosophila_melanogaster	az2	FBGN0025185
drosophila_melanogaster	CG2129	FBGN0030008
drosophila_melanogaster	CG1602	FBGN0033186
drosophila_melanogaster	CG18011	FBGN0033491
drosophila_melanogaster	CG12942	FBGN0033569
drosophila_melanogaster	indra	FBGN0035213
drosophila_melanogaster	CG30020	FBGN0050020
drosophila_melanogaster	mld	FBGN0263490
caenorhabditis_elegans	ztf-15	WBGENE00011066
caenorhabditis_elegans		WBGENE00015649

Paralogs (36): ZNF184 (ENSG00000096654), CTCF (ENSG00000102974), ZNF574 (ENSG00000105732), ZBTB24 (ENSG00000112365), ZNF142 (ENSG00000115568), CTCFL (ENSG00000124092), ZNF473 (ENSG00000142528), ZNF827 (ENSG00000151612), ZNF689 (ENSG00000156853), ZNF208 (ENSG00000160321), ZNF91 (ENSG00000167232), ZNF526 (ENSG00000167625), ZNF764 (ENSG00000169951), ZNF747 (ENSG00000169955), ZNF282 (ENSG00000170265), ZNF160 (ENSG00000170949), ZNF497 (ENSG00000174586), ZBTB34 (ENSG00000177125), ZNF771 (ENSG00000179965), ZNF48 (ENSG00000180035), ZNF594 (ENSG00000180626), ZBTB37 (ENSG00000185278), ZFP92 (ENSG00000189420), ZNF107 (ENSG00000196247), ZNF729 (ENSG00000196350), ZNF569 (ENSG00000196437), ZNF420 (ENSG00000197050), ZNF785 (ENSG00000197162), ZNF665 (ENSG00000197497), ZNF181 (ENSG00000197841), ZNF347 (ENSG00000197937), ZNF84 (ENSG00000198040), ZBTB48 (ENSG00000204859), ZNF845 (ENSG00000213799), ZNF99 (ENSG00000213973), ZNF688 (ENSG00000229809)

Protein

Protein identifiers

Zinc finger protein 302 — Q9NR11 (reviewed: Q9NR11)

Alternative names: Zinc finger protein 135-like, Zinc finger protein 140-like, Zinc finger protein 327

All UniProt accessions (8): Q9NR11, A0A087WYF4, B4DMN2, D6R9Q0, D6RA23, D6RAM0, E7EVR1, V9GYY2

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?
Q9NR11-1	1	yes
Q9NR11-2	2

RefSeq proteins (15): NP_001012320, NP_001276110, NP_001276111, NP_001276112, NP_001276113, NP_001276114, NP_001276115, NP_001276116, NP_001276117, NP_001276118, NP_001276119, NP_001276120, NP_001276121, NP_060913, NP_061145 (=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 (16 total): zinc finger region 7, sequence conflict 5, chain 1, domain 1, splice variant 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NR11-F1	60.12	0.04

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): 183

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 129 (showing top): DELYS_THYROID_CANCER_DN, LIAO_METASTASIS, DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP, KIM_WT1_TARGETS_DN, NUYTTEN_NIPP1_TARGETS_DN, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP, HORIUCHI_WTAP_TARGETS_UP, ZWANG_DOWN_BY_2ND_EGF_PULSE, CSR_EARLY_UP.V1_DN, GCM_RAB10, SHEN_SMARCA2_TARGETS_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

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 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), 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
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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

24 interactions, top by confidence:

A	B	Type	Score
CEP70	ZNF302	psi-mi:“MI:0915”(physical association)	0.670
ZNF302	CEP70	psi-mi:“MI:0915”(physical association)	0.670
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF302	NUP210	psi-mi:“MI:0915”(physical association)	0.400
ZNF302	SH3GLB2	psi-mi:“MI:0915”(physical association)	0.400
ZNF302		psi-mi:“MI:0915”(physical association)	0.370
	ZNF302	psi-mi:“MI:0915”(physical association)	0.370
CLIC1	ZNF302	psi-mi:“MI:0915”(physical association)	0.370
CAND1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
COPS5	FBLL1	psi-mi:“MI:0914”(association)	0.350
CBX5	ZNF568	psi-mi:“MI:0914”(association)	0.350
RFPL4B	KRBA1	psi-mi:“MI:0914”(association)	0.350
ZNF302	DMC1	psi-mi:“MI:0914”(association)	0.350
SLC1A3	DDX11L8	psi-mi:“MI:0914”(association)	0.350
EPHA1	ZNF302	psi-mi:“MI:0915”(physical association)	0.000
APP	ZNF302	psi-mi:“MI:0915”(physical association)	0.000
RBM11	ZNF302	psi-mi:“MI:0915”(physical association)	0.000
ZNF302	OPTN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (33): CEP70 (Two-hybrid), ZNF302 (Two-hybrid), TMEM25 (Affinity Capture-MS), ZNF302 (Affinity Capture-MS), TMEM25 (Affinity Capture-MS), ZNF302 (Affinity Capture-MS), DMC1 (Affinity Capture-MS), KRTAP10-6 (Two-hybrid), ZNF302 (Proximity Label-MS), ZNF302 (Two-hybrid), ZNF302 (Two-hybrid), ZNF302 (Two-hybrid), TMEM25 (Affinity Capture-MS), ZNF302 (Affinity Capture-MS), DMC1 (Affinity Capture-MS)

ESM2 similar proteins: A1KXM5, A1YFC1, A1YGK6, A2T7F2, A7KBS4, B2RXC5, E1JH25, G3X9G7, O96001, P16531, P18748, P34307, P88825, Q2EI21, Q3URU2, Q3V0C1, Q4V8E9, Q5JRM2, Q5R7U0, Q5RDG2, Q5RE50, Q5REF1, Q5SRN2, Q5SS00, Q5U4C1, Q6H236, Q6P1M9, Q6ZN11, Q810T2, Q8BUY8, Q8N3K9, Q8N660, Q8N720, Q8N859, Q8R2V3, Q920R4, Q921B4, Q923B3, Q95JY5, Q96D09

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

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	64
Likely benign	5
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1435 predictions. Top by Δscore:

Variant	Effect	Δscore
19:34681515:G:GT	donor_gain	1.0000
19:34677781:C:G	donor_gain	0.9900
19:34677861:GT:G	donor_gain	0.9900
19:34678812:AGGTA:A	donor_loss	0.9900
19:34678813:GGT:G	donor_loss	0.9900
19:34678814:G:T	donor_loss	0.9900
19:34678815:T:G	donor_loss	0.9900
19:34681483:GGA:G	donor_gain	0.9900
19:34681484:G:T	donor_gain	0.9900
19:34681490:T:G	donor_gain	0.9900
19:34681497:G:GT	donor_gain	0.9900
19:34681515:G:T	donor_gain	0.9900
19:34681522:G:GT	donor_gain	0.9900
19:34681522:G:T	donor_gain	0.9900
19:34681576:GCAT:G	donor_gain	0.9900
19:34681577:C:T	donor_gain	0.9900
19:34681593:G:GT	donor_gain	0.9900
19:34681595:A:T	donor_gain	0.9900
19:34681632:G:GG	donor_gain	0.9900
19:34677883:GGC:G	donor_gain	0.9800
19:34678635:C:T	donor_gain	0.9800
19:34682771:TTTCA:T	acceptor_loss	0.9800
19:34682774:CAG:C	acceptor_loss	0.9800
19:34682775:A:T	acceptor_loss	0.9800
19:34682893:TGTAG:T	donor_loss	0.9800
19:34682896:AGG:A	donor_loss	0.9800
19:34682897:GGTAA:G	donor_loss	0.9800
19:34682898:G:GT	donor_loss	0.9800
19:34682899:T:TC	donor_loss	0.9800
19:34677720:C:G	donor_gain	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000193422 (19:34681110 C>G), RS1000519672 (19:34682413 TTAGC>T), RS1001348574 (19:34677373 C>A,T), RS1001570216 (19:34686486 A>C,G), RS1002175512 (19:34676665 C>T), RS1002276664 (19:34682358 A>T), RS1002413876 (19:34682090 CAA>C), RS1002519345 (19:34674938 C>A), RS1002522651 (19:34685235 T>C), RS1003054717 (19:34685518 C>G,T), RS1003083281 (19:34678943 T>C), RS1003190905 (19:34675267 G>A), RS1003390299 (19:34686764 C>T), RS1003828094 (19:34680485 C>A), RS1004195176 (19:34676726 T>G)

Disease associations

OMIM: gene MIM:621271 | 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
Valproic Acid	decreases expression	4
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
motexafin gadolinium	increases expression	1
Acetaminophen	decreases expression	1
Benzene	increases expression	1
Benzo(a)pyrene	increases methylation	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Manganese	decreases expression, increases abundance	1
Methyl Methanesulfonate	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin M1	decreases expression	1
Cadmium Chloride	decreases expression	1
Zinc Acetate	increases 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_XW31	HEK293 eGFP-ZNF302	Transformed cell line	Female

Clinical trials (associated diseases)

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