ZNF320

Summary

ZNF320 (zinc finger protein 320, HGNC:13842) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 320 (A2RRD8). May be involved in transcriptional regulation.

ZNF320 encodes a Kruppel-like zinc finger protein. Members of this protein family are involved in activation or repression of transcription.

Source: NCBI Gene 162967 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 74 total
• MANE Select transcript: NM_001351774

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13842
Approved symbol	ZNF320
Name	zinc finger protein 320
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	ZFPL, DKFZp686G16228
Ensembl gene	ENSG00000182986
Ensembl biotype	protein_coding
OMIM	606427
Entrez	162967

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 27 protein_coding, 6 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000391781, ENST00000593618, ENST00000594408, ENST00000594741, ENST00000595202, ENST00000595635, ENST00000596215, ENST00000597091, ENST00000597111, ENST00000597265, ENST00000597856, ENST00000598199, ENST00000600930, ENST00000601334, ENST00000673631, ENST00000682928, ENST00000855873, ENST00000855874, ENST00000855875, ENST00000855876, ENST00000855877, ENST00000855878, ENST00000855879, ENST00000919701, ENST00000919702, ENST00000919703, ENST00000919704, ENST00000919705, ENST00000919706, ENST00000919707, ENST00000919708, ENST00000919709, ENST00000919710, ENST00000952398

RefSeq mRNA: 14 — MANE Select: NM_001351774 NM_001351773, NM_001351774, NM_001351775, NM_001351776, NM_001351777, NM_001387570, NM_001387571, NM_001387572, NM_001387573, NM_001387574, NM_001387575, NM_001387576, NM_001387577, NM_207333

CCDS: CCDS33095, CCDS92678

Canonical transcript exons

ENST00000682928 — 6 exons

Exon	Start	End
ENSE00003167046	52897520	52897635
ENSE00003173698	52891229	52891346
ENSE00003173861	52893779	52893856
ENSE00003226247	52876180	52881983
ENSE00003796257	52890241	52890328
ENSE00003896264	52888127	52888253

Expression profiles

Bgee: expression breadth ubiquitous, 239 present calls, max score 97.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1599 / max 149.6492, expressed in 1584 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182537	10.1599	1584

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.94	gold quality
oviduct epithelium	UBERON:0004804	96.30	gold quality
pancreatic ductal cell	CL:0002079	92.93	gold quality
tendon of biceps brachii	UBERON:0008188	89.76	gold quality
endometrium	UBERON:0001295	89.28	gold quality
right uterine tube	UBERON:0001302	88.95	gold quality
epithelial cell of pancreas	CL:0000083	88.64	gold quality
metanephros cortex	UBERON:0010533	87.23	gold quality
germinal epithelium of ovary	UBERON:0001304	87.12	gold quality
fallopian tube	UBERON:0003889	86.79	gold quality
ganglionic eminence	UBERON:0004023	86.75	gold quality
cortical plate	UBERON:0005343	86.60	gold quality
endothelial cell	CL:0000115	86.56	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.95	gold quality
colonic epithelium	UBERON:0000397	85.89	gold quality
cerebellar hemisphere	UBERON:0002245	85.72	gold quality
stromal cell of endometrium	CL:0002255	85.65	gold quality
cerebellar cortex	UBERON:0002129	85.49	gold quality
uterus	UBERON:0000995	85.20	gold quality
ovary	UBERON:0000992	85.06	gold quality
body of uterus	UBERON:0009853	84.99	gold quality
right ovary	UBERON:0002118	84.80	gold quality
body of pancreas	UBERON:0001150	84.75	gold quality
left ovary	UBERON:0002119	84.63	gold quality
islet of Langerhans	UBERON:0000006	84.57	gold quality
urinary bladder	UBERON:0001255	84.51	gold quality
cerebellum	UBERON:0002037	84.51	gold quality
pancreas	UBERON:0001264	84.48	gold quality
ileal mucosa	UBERON:0000331	84.43	gold quality
female reproductive system	UBERON:0000474	84.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.26

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1976.1	ZNF320	More than 3 adjacent zinc fingers
MA1976.2	ZNF320	More than 3 adjacent zinc fingers
MA1976.3	ZNF320	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:28273063

miRNA regulators (miRDB)

123 targeting ZNF320, 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-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6844	99.82	70.69	2423

Literature-anchored findings (GeneRIF, showing 1)

• ZNF320 is a hypomethylated prognostic biomarker involved in immune infiltration of hepatocellular carcinoma and associated with cell cycle. (PMID:36287187)

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 320 — A2RRD8 (reviewed: A2RRD8)

All UniProt accessions (7): A0A669KBJ2, A2RRD8, M0QX96, M0QZA2, M0R0Z8, M0R1K6, M0R2L4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Expressed at high levels in placenta, pancreas, kidney and heart, and at lower levels in liver, skeletal muscle and brain.

Disease relevance. A chromosomal aberration involving ZNF320 is found in a form of glioblastoma. Translocation t(10;19)(q26;q13.3) with BRWD2/WDR11.

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

RefSeq proteins (14): NP_001338702, NP_001338703, NP_001338704, NP_001338705, NP_001338706, NP_001374499, NP_001374500, NP_001374501, NP_001374502, NP_001374503, NP_001374504, NP_001374505, NP_001374506, NP_997216 (=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
IPR050589	Ikaros_C2H2-ZF	Family

Pfam: PF00096, PF01352

UniProt features (14 total): zinc finger region 12, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A2RRD8-F1	69.03	0.15

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: 41 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, BASAKI_YBX1_TARGETS_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, REACTOME_EPIGENETIC_REGULATION_OF_GENE_EXPRESSION, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, E2F2_TARGET_GENES, NFE2L1_TARGET_GENES, NFKBIA_TARGET_GENES, ZNF407_TARGET_GENES, MIR3646, MIR19A_3P, MIR19B_3P, MIR513A_3P_MIR513C_3P, MIR3133

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

Protein interactions and networks

STRING

538 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF320	DMBT1	Q9UGM3	825
ZNF320	PLAC8L1	A1L4L8	432
ZNF320	LGALS16	A8MUM7	426
ZNF320	MYEOV	Q96EZ4	382
ZNF320	CLC	Q05315	351
ZNF320	RNFT2	Q96EX2	324
ZNF320	KRTAP3-3	Q9BYR6	316
ZNF320	C9JR48	C9JR48	305
ZNF320	TCEAL9	Q9UHQ7	296
ZNF320	ERICH1	Q86X53	291
ZNF320	TTC5	Q8N0Z6	290
ZNF320	ENKUR	Q8TC29	280
ZNF320	MRPS25	P82663	278
ZNF320	MRPS9	P82933	276
ZNF320	RPL7L1	Q6DKI1	272

IntAct

32 interactions, top by confidence:

A	B	Type	Score
ZNF320	KRTAP10-5	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-7	ZNF320	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-5	ZNF320	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF320	PPM1G	psi-mi:“MI:0914”(association)	0.350
RPL34	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL27A	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPS19	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL7L1	ZNF320	psi-mi:“MI:0914”(association)	0.350
PURG	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF467	ZNF320	psi-mi:“MI:0914”(association)	0.350
FBLN5	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZKSCAN8	ZNF320	psi-mi:“MI:0914”(association)	0.350
GOLGA8A	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF460	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350
SPANXN2	ZNF320	psi-mi:“MI:0914”(association)	0.350
ZNF677	ZNF320	psi-mi:“MI:0914”(association)	0.350
TIMM50	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPLP0	ZNF320	psi-mi:“MI:0914”(association)	0.350
RBM4B	ZNF320	psi-mi:“MI:0914”(association)	0.350
RPL4	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (29): KRTAP10-7 (Two-hybrid), KRTAP10-5 (Two-hybrid), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS), ZNF320 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2PQL4, A0JPL0, A2RRD8, A6NHJ4, A6NP11, B4DX44, O75346, O95780, P0CB33, P21506, P51508, P52738, Q0D2J5, Q0VGE8, Q12901, Q13360, Q14593, Q15973, Q2M218, Q2M3X9, Q2VY69, Q3SXZ3, Q5HY98, Q5RCJ2, Q5VIY5, Q6J6I6, Q7L2R6, Q86XU0, Q86Y25, Q8IW36, Q8IYN0, Q8IYX0, Q8N782, Q8N883, Q8N9Z0, Q8NDP4, Q95K49, Q969W8, Q96H40, Q96N58

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 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
Peptide chain elongation	5	37.3×	3e-06
Viral mRNA Translation	5	37.3×	3e-06
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	36.9×	3e-06
Selenocysteine synthesis	5	35.4×	3e-06
Eukaryotic Translation Termination	5	35.4×	3e-06
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5	34.6×	3e-06
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	5	34.6×	3e-06
Formation of a pool of free 40S subunits	5	32.9×	3e-06

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	5	46.3×	8e-06
translation	5	25.7×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	58
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1237 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52881981:TAT:T	acceptor_gain	1.0000
19:52888119:AT:A	donor_gain	1.0000
19:52888249:AGACC:A	acceptor_gain	1.0000
19:52888250:GACC:G	acceptor_gain	1.0000
19:52888252:CC:C	acceptor_gain	1.0000
19:52888253:CC:C	acceptor_gain	1.0000
19:52888253:CCT:C	acceptor_loss	1.0000
19:52888254:C:CC	acceptor_gain	1.0000
19:52888254:C:T	acceptor_gain	1.0000
19:52888254:CTG:C	acceptor_loss	1.0000
19:52888254:CTGAA:C	acceptor_loss	1.0000
19:52888255:T:C	acceptor_loss	1.0000
19:52890237:TCA:T	donor_loss	1.0000
19:52890238:CA:C	donor_loss	1.0000
19:52890240:C:CG	donor_loss	1.0000
19:52890324:CAATC:C	acceptor_gain	1.0000
19:52890327:TC:T	acceptor_gain	1.0000
19:52890328:CC:C	acceptor_gain	1.0000
19:52890329:CTAA:C	acceptor_loss	1.0000
19:52890330:T:G	acceptor_loss	1.0000
19:52881979:GATAT:G	acceptor_gain	0.9900
19:52881984:C:CC	acceptor_gain	0.9900
19:52881985:T:G	acceptor_loss	0.9900
19:52888097:T:TA	donor_gain	0.9900
19:52888098:C:A	donor_gain	0.9900
19:52888121:CCTCA:C	donor_loss	0.9900
19:52888122:CTCAC:C	donor_loss	0.9900
19:52888123:TCA:T	donor_loss	0.9900
19:52888124:C:CC	donor_loss	0.9900
19:52888125:A:AC	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000047732 (19:52899683 G>A), RS1000188425 (19:52894365 CAG>C), RS1000220927 (19:52894618 A>T), RS1000280717 (19:52859069 A>G), RS1000523924 (19:52895805 G>T), RS1000554677 (19:52902887 A>C), RS1000555241 (19:52896098 T>C), RS1000568923 (19:52859582 G>A), RS1000606656 (19:52901421 G>A,T), RS1000646951 (19:52897272 C>A), RS1000648066 (19:52860017 A>G), RS1000772864 (19:52864314 A>G), RS1000832948 (19:52889709 A>G,T), RS1000861766 (19:52892668 A>G), RS1000904920 (19:52902491 C>G,T)

Disease associations

OMIM: gene MIM:606427 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001282_3	Psychosis in Alzheimer’s disease	5.000000e-06
GCST90002393_671	Monocyte count	2.000000e-12
GCST90002400_96	Plateletcrit	4.000000e-13

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005940	psychotic symptoms
EFO:0005091	monocyte count
EFO:0007985	platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Air Pollutants	affects expression, increases abundance, decreases expression	2
Endosulfan	decreases expression, increases expression	2
Aflatoxin B1	increases methylation	2
Particulate Matter	decreases expression, increases abundance, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	increases expression	1
di-n-butylphosphoric acid	affects expression	1
Resveratrol	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Arbutin	decreases expression	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Vehicle Emissions	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Polychlorinated Biphenyls	affects expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Vanadates	decreases expression	1
Aflatoxin M1	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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