ZNF391

Summary

ZNF391 (zinc finger protein 391, HGNC:18779) is a protein-coding gene on chromosome 6p22.1, encoding Zinc finger protein 391 (Q9UJN7). 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 346157 — RefSeq curated summary.

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 49 total
• MANE Select transcript: NM_001076781

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18779
Approved symbol	ZNF391
Name	zinc finger protein 391
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	dJ153G14.3
Ensembl gene	ENSG00000124613
Ensembl biotype	protein_coding
Entrez	346157

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 8 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000244576, ENST00000461521, ENST00000477999, ENST00000482767, ENST00000901127, ENST00000901128, ENST00000901129, ENST00000937720, ENST00000937721, ENST00000958924

RefSeq mRNA: 4 — MANE Select: NM_001076781 NM_001076781, NM_001322288, NM_001322289, NM_001322293

CCDS: CCDS43429

Canonical transcript exons

ENST00000244576 — 3 exons

Exon	Start	End
ENSE00001426539	27388759	27389075
ENSE00001537391	27399442	27399550
ENSE00001733042	27400293	27403908

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 84.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 2.2089 / max 65.0649, expressed in 938 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66567	0.8998	469
66570	0.8979	502
66568	0.2293	110
66569	0.1557	80
66566	0.0262	7

Top tissues by expression

284 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	84.35	gold quality
right uterine tube	UBERON:0001302	79.40	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.09	gold quality
cerebellar hemisphere	UBERON:0002245	73.84	gold quality
prefrontal cortex	UBERON:0000451	73.79	gold quality
cerebellar cortex	UBERON:0002129	73.77	gold quality
right hemisphere of cerebellum	UBERON:0014890	73.76	gold quality
body of pancreas	UBERON:0001150	73.42	gold quality
left ovary	UBERON:0002119	73.25	gold quality
right ovary	UBERON:0002118	72.79	gold quality
cortical plate	UBERON:0005343	72.70	gold quality
right frontal lobe	UBERON:0002810	72.49	gold quality
Brodmann (1909) area 9	UBERON:0013540	72.44	gold quality
anterior cingulate cortex	UBERON:0009835	71.87	gold quality
cingulate cortex	UBERON:0003027	71.77	gold quality
ventricular zone	UBERON:0003053	71.44	gold quality
cerebellum	UBERON:0002037	71.27	gold quality
pancreas	UBERON:0001264	71.10	gold quality
right lobe of thyroid gland	UBERON:0001119	71.02	gold quality
endocervix	UBERON:0000458	70.99	gold quality
descending thoracic aorta	UBERON:0002345	70.94	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	70.86	gold quality
islet of Langerhans	UBERON:0000006	70.71	gold quality
right adrenal gland cortex	UBERON:0035827	70.63	gold quality
left testis	UBERON:0004533	70.62	gold quality
left lobe of thyroid gland	UBERON:0001120	70.61	gold quality
right testis	UBERON:0004534	70.57	gold quality
right coronary artery	UBERON:0001625	70.53	gold quality
ganglionic eminence	UBERON:0004023	70.46	gold quality
nucleus accumbens	UBERON:0001882	70.41	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

118 targeting ZNF391, 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-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-6809-3P	99.91	71.45	3814

Literature-anchored findings (GeneRIF, showing 1)

• Spatial Expression Pattern of ZNF391 Gene in the Brains of Patients With Schizophrenia, Bipolar Disorders or Major Depressive Disorder Identifies New Cross-Disorder Biotypes: A Trans-Diagnostic, Top-Down Approach. (PMID:33822213)

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), 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 391 — Q9UJN7 (reviewed: Q9UJN7)

All UniProt accessions (2): C9JUF8, Q9UJN7

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 (4): NP_001070249, NP_001309217, NP_001309218, NP_001309222 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (17 total): zinc finger region 9, compositionally biased region 3, region of interest 2, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJN7-F1	76.74	0.65

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 81 (showing top): BROWNE_HCMV_INFECTION_12HR_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, ARNT2_TARGET_GENES, CBX5_TARGET_GENES, CHAMP1_TARGET_GENES, CREB3L4_TARGET_GENES, DIDO1_TARGET_GENES, GLI4_TARGET_GENES, HES2_TARGET_GENES, HMG20B_TARGET_GENES, KLF14_TARGET_GENES, KLF7_TARGET_GENES, RLF_TARGET_GENES

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

GO Molecular Function (5): 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), 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
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
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

244 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF391	KRABD4	Q5JUW0	638
ZNF391	OR2H1	Q9GZK4	574
ZNF391	SAPCD1	Q5SSQ6	542
ZNF391	LRRC36	Q1X8D7	400
ZNF391	SPRYD4	Q8WW59	399
ZNF391	C5orf34	Q96MH7	399
ZNF391	GBX1	Q14549	358
ZNF391	MRPS11	P82912	356
ZNF391	CALHM2	Q9HA72	349
ZNF391	ABHD3	Q8WU67	335
ZNF391	NELFE	P18615	323
ZNF391	TMEM178A	Q8NBL3	322
ZNF391	MRPL42	Q9Y6G3	320
ZNF391	PNPLA7	Q6ZV29	314
ZNF391	SLC25A26	Q70HW3	311
ZNF391	PTOV1	Q86YD1	311

IntAct

0 interactions, top by confidence:

BioGRID (8): ZNF391 (Two-hybrid), ZNF391 (Two-hybrid), ZNF391 (Two-hybrid), ZNF391 (Two-hybrid), ZNF391 (Two-hybrid), ZNF391 (Affinity Capture-MS), ZNF391 (Affinity Capture-MS), ZNF391 (Affinity Capture-MS)

ESM2 similar proteins: A0JNB1, A6QLU5, O75123, O75820, P10076, P10755, P16374, P17031, P17097, P17141, P51814, Q02975, Q08ER8, Q14588, Q14590, Q32KN0, Q3V080, Q4V8A8, Q5CZA5, Q5R4K8, Q5R5Q6, Q5R9S5, Q5RBX0, Q61751, Q6GQR8, Q6P560, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q7Z3V5, Q8BLB0, Q8N141, Q8N184, Q8N823, Q8N8J6, Q8N9F8, Q8TBZ5, Q8TF47, Q96ND8

Diamond homologs: A0A087WUV0, Q96K75, Q99676, Q9HBT8, Q9UJL9, Q9UJN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

600 predictions. Top by Δscore:

Variant	Effect	Δscore
6:27397583:G:GG	donor_gain	0.9800
6:27397582:A:AG	donor_gain	0.9700
6:27400292:GATA:G	acceptor_gain	0.9700
6:27388877:G:GT	donor_gain	0.9500
6:27399551:G:GG	donor_gain	0.9500
6:27399547:CTTGG:C	donor_loss	0.9400
6:27399548:TTGGT:T	donor_loss	0.9400
6:27399549:TGGTG:T	donor_loss	0.9400
6:27399551:GT:G	donor_loss	0.9400
6:27399552:T:TA	donor_loss	0.9400
6:27399553:GAGTA:G	donor_loss	0.9400
6:27399554:AG:A	donor_loss	0.9400
6:27399555:G:A	donor_loss	0.9400
6:27388983:T:TA	donor_gain	0.9200
6:27399436:CTGCA:C	acceptor_loss	0.9200
6:27399437:TGCA:T	acceptor_loss	0.9200
6:27399438:GCAGG:G	acceptor_loss	0.9200
6:27399439:CA:C	acceptor_loss	0.9200
6:27399440:A:G	acceptor_loss	0.9200
6:27399441:G:C	acceptor_loss	0.9200
6:27400287:TTTCA:T	acceptor_loss	0.9200
6:27400288:TTCA:T	acceptor_loss	0.9200
6:27400289:TCAGA:T	acceptor_loss	0.9200
6:27400291:AG:A	acceptor_loss	0.9200
6:27388925:TTCG:T	donor_gain	0.9100
6:27388984:T:A	donor_gain	0.9100
6:27399556:T:G	donor_loss	0.9100
6:27389043:GGTG:G	donor_loss	0.9000
6:27389044:G:GA	donor_loss	0.9000
6:27389045:T:TT	donor_loss	0.9000

AlphaMissense

2387 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:27400890:T:C	F174L	0.998
6:27400892:T:A	F174L	0.998
6:27400892:T:G	F174L	0.998
6:27400974:T:C	F202L	0.998
6:27400976:T:A	F202L	0.998
6:27400976:T:G	F202L	0.998
6:27400806:T:C	F146L	0.997
6:27400808:C:A	F146L	0.997
6:27400808:C:G	F146L	0.997
6:27401310:T:C	F314L	0.996
6:27401312:C:A	F314L	0.996
6:27401312:C:G	F314L	0.996
6:27401394:T:C	F342L	0.996
6:27401396:C:A	F342L	0.996
6:27401396:C:G	F342L	0.996
6:27400897:G:C	R176P	0.995
6:27401142:T:C	F258L	0.995
6:27401144:C:A	F258L	0.995
6:27401144:C:G	F258L	0.995
6:27400825:T:C	L152P	0.994
6:27400981:G:C	R204P	0.994
6:27400993:T:C	L208P	0.994
6:27401003:T:A	H211Q	0.994
6:27401003:T:G	H211Q	0.994
6:27400813:G:C	R148P	0.993
6:27400835:T:A	H155Q	0.993
6:27400835:T:G	H155Q	0.993
6:27400891:T:C	F174S	0.993
6:27401008:G:C	R213P	0.993
6:27401058:T:C	F230L	0.993

dbSNP variants (sampled 300 via entrez): RS1000018252 (6:27372807 G>A), RS1000164453 (6:27401337 C>T), RS1000220226 (6:27388971 A>G,T), RS1000263524 (6:27393621 C>T), RS1000308850 (6:27402091 G>C), RS1000335921 (6:27381519 G>A,T), RS1000337516 (6:27393988 T>C), RS1000841722 (6:27381188 G>A), RS1001096943 (6:27374969 T>A), RS1001384925 (6:27388209 A>G), RS1001427217 (6:27374665 C>G), RS1001566301 (6:27402843 C>T), RS1001572538 (6:27378583 C>T), RS1001580246 (6:27403671 T>G), RS1001663818 (6:27397067 G>A)

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

21 associations (top):

Study	Trait	p-value
GCST004521_116	Autism spectrum disorder or schizophrenia	3.000000e-16
GCST004521_166	Autism spectrum disorder or schizophrenia	4.000000e-24
GCST004521_254	Autism spectrum disorder or schizophrenia	6.000000e-11
GCST004521_57	Autism spectrum disorder or schizophrenia	1.000000e-20
GCST004521_69	Autism spectrum disorder or schizophrenia	8.000000e-24
GCST004521_73	Autism spectrum disorder or schizophrenia	8.000000e-11
GCST006948_35	Feeling nervous	5.000000e-08
GCST008921_6	Asthma and major depressive disorder	1.000000e-09
GCST008921_9	Asthma and major depressive disorder	3.000000e-08
GCST010002_50	Refractive error	4.000000e-34
GCST010142_16	Fish- and plant-related diet	2.000000e-10
GCST010142_19	Fish- and plant-related diet	4.000000e-10
GCST010142_34	Fish- and plant-related diet	7.000000e-09
GCST010142_35	Fish- and plant-related diet	8.000000e-09
GCST010142_42	Fish- and plant-related diet	1.000000e-08
GCST010142_7	Fish- and plant-related diet	3.000000e-12
GCST010702_75	Subcortical volume (MOSTest)	3.000000e-11
GCST010703_272	Brain morphology (MOSTest)	7.000000e-16
GCST90011899_28	Aspartate aminotransferase levels	8.000000e-30
GCST90011900_180	Serum alkaline phosphatase levels	1.000000e-10
GCST90016674_15	Liver iron content	2.000000e-29

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0009597	feeling nervous measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004736	aspartate aminotransferase measurement
EFO:0004533	alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects methylation, decreases expression, affects cotreatment, increases abundance, increases expression	3
Valproic Acid	decreases expression	3
bisphenol A	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
manganese chloride	affects cotreatment, increases abundance, increases expression	1
perfluorooctane sulfonic acid	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
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	decreases methylation, affects cotreatment	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	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_HD24	HEK293 eGFP-ZNF391	Transformed cell line	Female

Clinical trials (associated diseases)

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