ZNF30

Summary

ZNF30 (zinc finger protein 30, HGNC:13090) is a protein-coding gene on chromosome 19q13.13, encoding Zinc finger protein 30 (P17039). 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 90075 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 97 total
• MANE Select transcript: NM_194325

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13090
Approved symbol	ZNF30
Name	zinc finger protein 30
Location	19q13.13
Locus type	gene with protein product
Status	Approved
Aliases	KOX28, DKFZp686N19164, FLJ20562
Ensembl gene	ENSG00000168661
Ensembl biotype	protein_coding
Entrez	90075

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 11 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000303586, ENST00000439785, ENST00000595818, ENST00000601142, ENST00000601540, ENST00000601957, ENST00000891913, ENST00000891914, ENST00000932306, ENST00000932307, ENST00000957110, ENST00000957111

RefSeq mRNA: 3 — MANE Select: NM_194325 NM_001099437, NM_001099438, NM_194325

CCDS: CCDS46044, CCDS46045

Canonical transcript exons

ENST00000601142 — 5 exons

Exon	Start	End
ENSE00001734895	34926903	34927216
ENSE00003211754	34943223	34945168
ENSE00003573321	34933628	34933723
ENSE00003706249	34929884	34929956
ENSE00003709229	34931843	34931993

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 86.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.6811 / max 43.0608, expressed in 1175 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175157	1.0046	564
175158	0.8472	483
175160	0.6337	354
175159	0.1955	82

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.07	gold quality
secondary oocyte	CL:0000655	85.17	gold quality
epithelial cell of pancreas	CL:0000083	84.40	silver quality
Brodmann (1909) area 23	UBERON:0013554	83.67	gold quality
tendon of biceps brachii	UBERON:0008188	83.40	silver quality
middle temporal gyrus	UBERON:0002771	82.93	silver quality
cerebellar cortex	UBERON:0002129	82.11	gold quality
cerebellar hemisphere	UBERON:0002245	82.08	gold quality
cerebellum	UBERON:0002037	81.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.60	gold quality
tibia	UBERON:0000979	80.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.18	gold quality
primary visual cortex	UBERON:0002436	79.00	gold quality
endothelial cell	CL:0000115	78.67	gold quality
pancreatic ductal cell	CL:0002079	78.28	gold quality
cortical plate	UBERON:0005343	78.10	gold quality
cerebellar vermis	UBERON:0004720	77.34	gold quality
pigmented layer of retina	UBERON:0001782	77.30	gold quality
visceral pleura	UBERON:0002401	77.16	gold quality
germinal epithelium of ovary	UBERON:0001304	76.80	gold quality
parietal pleura	UBERON:0002400	76.49	gold quality
apex of heart	UBERON:0002098	75.66	gold quality
palpebral conjunctiva	UBERON:0001812	74.71	gold quality
ganglionic eminence	UBERON:0004023	74.48	gold quality
tendon	UBERON:0000043	74.41	gold quality
Brodmann (1909) area 9	UBERON:0013540	73.47	gold quality
occipital lobe	UBERON:0002021	73.38	gold quality
caudate nucleus	UBERON:0001873	73.34	gold quality
right frontal lobe	UBERON:0002810	73.13	gold quality
granulocyte	CL:0000094	73.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-100618	yes	651.73
E-ANND-3	no	3.81

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting ZNF30, 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-4682	100.00	68.89	1258
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-4762-3P	99.43	69.72	2363
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-1206	99.30	69.32	1016
HSA-MIR-4705	99.10	69.10	1091
HSA-MIR-4711-5P	98.89	68.00	965
HSA-MIR-6512-5P	98.76	69.29	1195
HSA-MIR-4266	98.53	67.29	1035
HSA-MIR-338-3P	98.14	67.38	1137
HSA-MIR-4303	98.01	68.13	2304
HSA-MIR-634	97.74	67.11	818
HSA-MIR-7112-3P	97.67	68.77	948
HSA-MIR-6500-3P	97.42	67.20	867

Cross-species orthologs

0 orthologs

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 30 — P17039 (reviewed: P17039)

Alternative names: Zinc finger protein KOX28

All UniProt accessions (2): P17039, V9GYJ2

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (3)

UniProt ID	Names	Canonical?
P17039-1	1	yes
P17039-2	2
P17039-3	3

RefSeq proteins (3): NP_001092907, NP_001092908, NP_919306* (*=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
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF01352

UniProt features (34 total): zinc finger region 18, sequence conflict 7, sequence variant 4, splice variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P17039-F1	79.09	0.22

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: 42 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ZWANG_DOWN_BY_2ND_EGF_PULSE, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, RYBP_TARGET_GENES, UBN1_TARGET_GENES, ZNF2_TARGET_GENES, ZNF30_TARGET_GENES, ZNF512_TARGET_GENES, ZSCAN21_TARGET_GENES, MIR23A_3P_MIR23B_3P, MIR23C, MIR4307, MIR4682, GSE13485_DAY1_VS_DAY3_YF17D_VACCINE_PBMC_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 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), sequence-specific DNA binding (GO:0043565), 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
DNA 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
ZNF30	SCGB2B2	Q4G0G5	475
ZNF30	TATDN2	Q93075	370
ZNF30	PHF8	Q9UPP1	359
ZNF30	TTK	P33981	352
ZNF30	ZNF385B	Q569K4	341
ZNF30	UBA2	Q9UBT2	323
ZNF30	C9JR48	C9JR48	322
ZNF30	ZDHHC8	Q9ULC8	315
ZNF30	YWHAE	P29360	314
ZNF30	LSM14A	Q8ND56	313
ZNF30	ZC3H4	Q9UPT8	311
ZNF30	PRSS33	Q8NF86	311
ZNF30	WTIP	A6NIX2	311
ZNF30	ZNF277	Q9NRM2	305
ZNF30	POGZ	Q7Z3K3	289

IntAct

7 interactions, top by confidence:

A	B	Type	Score
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF30	SPAST	psi-mi:“MI:0915”(physical association)	0.400
MRFAP1L1	MYO9A	psi-mi:“MI:0914”(association)	0.350
CLK2	CPSF4	psi-mi:“MI:0914”(association)	0.350

BioGRID (9): ZNF30 (Affinity Capture-MS), SPAST (Affinity Capture-MS), ZNF30 (Affinity Capture-MS), ZNF30 (Affinity Capture-MS), ZNF30 (Affinity Capture-MS), ZNF30 (Proximity Label-MS), ZNF30 (Cross-Linking-MS (XL-MS)), ZNF30 (Co-fractionation), ZNF30 (Affinity Capture-MS)

ESM2 similar proteins: A2VDQ7, A6NNF4, A8MQ14, A8MTY0, E9QAG8, O75290, O75373, P08043, P0CJ79, P10751, P17017, P17027, P17039, P35789, P51522, P51523, Q08AN1, Q14585, Q14587, Q3SYV7, Q3ZCX4, Q4R4C7, Q52M93, Q5MCW4, Q5R5U3, Q5R8X1, Q5R9F0, Q5SXM1, Q6ECI4, Q6JLC9, Q6P3V2, Q6P5C7, Q6ZN57, Q86UE3, Q86XN6, Q86YE8, Q8C827, Q8IYB9, Q8N4W9, Q8N7M2

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, E9Q8G5, O14628, O43345, O60765, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P10078, P17019, P17038, P17039, P35789, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

959 predictions. Top by Δscore:

Variant	Effect	Δscore
19:34927215:GC:G	donor_gain	1.0000
19:34929957:G:GG	donor_gain	1.0000
19:34931842:GAA:G	acceptor_gain	1.0000
19:34931842:GAAAT:G	acceptor_gain	1.0000
19:34931990:ATGG:A	donor_gain	1.0000
19:34931990:ATGGG:A	donor_loss	1.0000
19:34931991:TGG:T	donor_gain	1.0000
19:34931991:TGGG:T	donor_loss	1.0000
19:34931992:GG:G	donor_gain	1.0000
19:34931992:GGG:G	donor_gain	1.0000
19:34931992:GGGT:G	donor_loss	1.0000
19:34931993:GG:G	donor_gain	1.0000
19:34931993:GGT:G	donor_loss	1.0000
19:34931994:G:GG	donor_gain	1.0000
19:34931995:T:A	donor_loss	1.0000
19:34933608:C:G	acceptor_gain	1.0000
19:34933610:T:G	acceptor_gain	1.0000
19:34943221:A:AG	acceptor_gain	1.0000
19:34943222:G:GG	acceptor_gain	1.0000
19:34927204:GAC:G	donor_gain	0.9900
19:34927217:G:GG	donor_gain	0.9900
19:34929872:T:TA	acceptor_gain	0.9900
19:34929873:G:A	acceptor_gain	0.9900
19:34929882:A:AG	acceptor_gain	0.9900
19:34929883:G:GG	acceptor_gain	0.9900
19:34929883:GCTTT:G	acceptor_gain	0.9900
19:34929954:CATGT:C	donor_loss	0.9900
19:34929956:TG:T	donor_loss	0.9900
19:34929957:G:C	donor_loss	0.9900
19:34929958:T:A	donor_loss	0.9900

AlphaMissense

4145 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:34944191:T:C	F409L	0.994
19:34944193:T:A	F409L	0.994
19:34944193:T:G	F409L	0.994
19:34944611:T:C	F549L	0.994
19:34944613:T:A	F549L	0.994
19:34944613:T:G	F549L	0.994
19:34943855:T:C	F297L	0.993
19:34943857:T:A	F297L	0.993
19:34943857:T:G	F297L	0.993
19:34944527:T:C	F521L	0.993
19:34944529:C:A	F521L	0.993
19:34944529:C:G	F521L	0.993
19:34943939:T:C	F325L	0.992
19:34943941:C:A	F325L	0.992
19:34943941:C:G	F325L	0.992
19:34944023:T:C	F353L	0.992
19:34944025:T:A	F353L	0.992
19:34944025:T:G	F353L	0.992
19:34944359:T:C	F465L	0.992
19:34944361:C:A	F465L	0.992
19:34944361:C:G	F465L	0.992
19:34944695:T:C	F577L	0.992
19:34944697:T:A	F577L	0.992
19:34944697:T:G	F577L	0.992
19:34944107:T:C	F381L	0.991
19:34944109:C:A	F381L	0.991
19:34944109:C:G	F381L	0.991
19:34944275:T:C	F437L	0.990
19:34944277:T:A	F437L	0.990
19:34944277:T:G	F437L	0.990

dbSNP variants (sampled 300 via entrez): RS1000067119 (19:34924173 A>C), RS1000138655 (19:34925486 C>T), RS1000174088 (19:34943080 T>G), RS1000247261 (19:34942725 G>C), RS1000254528 (19:34937001 G>T), RS1000314817 (19:34942445 A>G), RS1000483398 (19:34936467 G>A,T), RS1000484142 (19:34944735 A>G), RS1000516327 (19:34944573 G>A), RS1000579247 (19:34941378 C>T), RS1000622009 (19:34937985 G>A), RS1000782662 (19:34936094 C>T), RS1000806813 (19:34935102 G>C), RS1001054739 (19:34941173 C>G,T), RS1001079513 (19:34932868 C>T)

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

1 associations (top):

Study	Trait	p-value
GCST006993_14	Hippocampal volume in Alzheimer’s disease dementia	6.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0005035	hippocampal volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	decreases methylation	1
beta-lapachone	increases expression, decreases expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
methacrylaldehyde	increases abundance, affects cotreatment, increases oxidation	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	increases expression, affects cotreatment	1
abrine	decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases oxidation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Cadmium	increases expression, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Ozone	increases oxidation, increases abundance, affects cotreatment	1
Potassium Chloride	decreases expression, decreases response to substance	1
Quercetin	decreases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression, decreases response to substance	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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