ZNF316

Summary

ZNF316 (zinc finger protein 316, HGNC:13843) is a protein-coding gene on chromosome 7p22.1, encoding Zinc finger protein 316 (A6NFI3). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and 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 100131017 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 10 total
• MANE Select transcript: NM_001278559

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13843
Approved symbol	ZNF316
Name	zinc finger protein 316
Location	7p22.1
Locus type	gene with protein product
Status	Approved
Aliases	MZF-3, ENST00000305834
Ensembl gene	ENSG00000205903
Ensembl biotype	protein_coding
Entrez	100131017

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 12 protein_coding, 1 retained_intron

ENST00000382252, ENST00000427912, ENST00000614588, ENST00000949893, ENST00000949894, ENST00000949895, ENST00000949896, ENST00000949897, ENST00000949898, ENST00000949899, ENST00000949900, ENST00000949901, ENST00000949902

RefSeq mRNA: 1 — MANE Select: NM_001278559 NM_001278559

CCDS: CCDS75563

Canonical transcript exons

ENST00000382252 — 9 exons

Exon	Start	End
ENSE00001491405	6652303	6658279
ENSE00001594433	6641825	6641962
ENSE00001637550	6639042	6639141
ENSE00001665488	6642382	6642764
ENSE00001753686	6637846	6638009
ENSE00001774138	6637318	6637447
ENSE00003558975	6643822	6643948
ENSE00003624307	6642964	6643073
ENSE00003684929	6644480	6644593

Expression profiles

Bgee: expression breadth ubiquitous, 221 present calls, max score 92.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.0125 / max 371.8702, expressed in 1803 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77165	11.0017	1783
77166	2.9882	1320
77164	1.0226	709

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	92.93	silver quality
granulocyte	CL:0000094	92.82	gold quality
right lobe of thyroid gland	UBERON:0001119	90.98	gold quality
left lobe of thyroid gland	UBERON:0001120	90.15	gold quality
sural nerve	UBERON:0015488	89.73	gold quality
thyroid gland	UBERON:0002046	89.25	gold quality
monocyte	CL:0000576	89.24	gold quality
leukocyte	CL:0000738	89.05	gold quality
body of uterus	UBERON:0009853	88.62	gold quality
spleen	UBERON:0002106	88.58	gold quality
vermiform appendix	UBERON:0001154	88.35	gold quality
cortical plate	UBERON:0005343	88.26	gold quality
stromal cell of endometrium	CL:0002255	87.87	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	87.81	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.80	gold quality
mucosa of stomach	UBERON:0001199	87.75	gold quality
caecum	UBERON:0001153	87.58	gold quality
skin of leg	UBERON:0001511	87.53	gold quality
right uterine tube	UBERON:0001302	87.37	gold quality
lower esophagus muscularis layer	UBERON:0035833	87.36	gold quality
lower esophagus	UBERON:0013473	87.35	gold quality
apex of heart	UBERON:0002098	87.32	gold quality
skin of abdomen	UBERON:0001416	87.13	gold quality
left uterine tube	UBERON:0001303	87.10	gold quality
right coronary artery	UBERON:0001625	87.01	gold quality
body of stomach	UBERON:0001161	86.84	gold quality
right adrenal gland cortex	UBERON:0035827	86.61	gold quality
small intestine Peyer’s patch	UBERON:0003454	86.58	gold quality
metanephros cortex	UBERON:0010533	86.56	gold quality
fundus of stomach	UBERON:0001160	86.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.32

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

4 targets.

Target	Regulation
PDLIM7
RGS2
S100A9
TRIM28

miRNA regulators (miRDB)

108 targeting ZNF316, 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-4283	100.00	66.42	2097
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-12118	100.00	65.88	1270
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-513B-5P	99.99	69.96	2150
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-8073	99.86	65.21	1118
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-320A-3P	99.77	69.73	2107
HSA-MIR-320B	99.77	69.73	2107
HSA-MIR-320C	99.77	69.73	2107
HSA-MIR-320D	99.77	69.73	2107
HSA-MIR-4429	99.77	69.62	2111
HSA-MIR-6764-5P	99.75	67.89	2304

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp316	ENSMUSG00000046658
rattus_norvegicus	Zfp316	ENSRNOG00000001094

Paralogs (1): ZNF787 (ENSG00000142409)

Protein

Protein identifiers

Zinc finger protein 316 — A6NFI3 (reviewed: A6NFI3)

All UniProt accessions (2): A0A087WZ61, A6NFI3

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 (1): NP_001265488* (*=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 (33 total): zinc finger region 15, compositionally biased region 6, modified residue 4, region of interest 3, cross-link 2, initiator methionine 1, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NFI3-F1	60.88	0.02

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): 2, 7, 10, 112, 829, 955

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): chr7p22, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN, CHYLA_CBFA2T3_TARGETS_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, FOXN3_TARGET_GENES, TFEB_TARGET_GENES, MIR6778_3P, MIR4283, MIR6842_3P, MIR7855_5P, MIR212_5P, MIR4795_5P, MIR4772_5P

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

GO Molecular Function (5): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), sequence-specific DNA binding (GO:0043565), 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
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
DNA binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

768 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF316	C2orf68	Q2NKX9	480
ZNF316	HDDC2	Q7Z4H3	462
ZNF316	PXDC1	Q5TGL8	415
ZNF316	F5GXR3	F5GXR3	374
ZNF316	METTL15	A6NJ78	370
ZNF316	ASCL5	Q7RTU5	370
ZNF316	ZNF512	Q96ME7	356
ZNF316	IGHV3-11	P01762	356
ZNF316	NDOR1	Q9UHB4	354
ZNF316	KCNN2	Q9H2S1	299
ZNF316	SLC25A31	Q9H0C2	282
ZNF316	COPG2	Q9UBF2	272
ZNF316	NEDD1	Q8NHV4	257
ZNF316	GPATCH8	Q9UKJ3	257
ZNF316	ABCA6	Q8N139	256

IntAct

76 interactions, top by confidence:

A	B	Type	Score
ZNF764	ZNF316	psi-mi:“MI:0914”(association)	0.640
ZNF764	SH3PXD2B	psi-mi:“MI:0914”(association)	0.530
ZNF169	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF324B	ZNF316	psi-mi:“MI:0914”(association)	0.530
ZNF707	ZNF316	psi-mi:“MI:0914”(association)	0.530
VWCE	ZNF316	psi-mi:“MI:0914”(association)	0.530
CACNG5	ZNF316	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
RPS3	ZNF316	psi-mi:“MI:0914”(association)	0.530
FBL	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
NOTCH2	ZNF316	psi-mi:“MI:0914”(association)	0.530
	ZNF316	psi-mi:“MI:0914”(association)	0.350
FBL	GXYLT2	psi-mi:“MI:0914”(association)	0.350
EFEMP1	ZNF316	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350

BioGRID (73): ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS), ZNF316 (Affinity Capture-MS)

ESM2 similar proteins: A0A2Z4LIS9, A2CE44, A6NFI3, E9PZZ1, O95201, P09066, P15863, P19622, P22091, P46099, P49640, P70338, P82976, P97503, P98168, P98169, Q05917, Q07120, Q13351, Q14549, Q14V87, Q15270, Q19A40, Q2QGD7, Q3SY56, Q3U133, Q58DK7, Q5DWN0, Q6IQX8, Q6NUN9, Q8C8V1, Q8NCA9, Q8TD94, Q8WUU4, Q924A2, Q92618, Q96RK0, Q99684, Q9BV97, Q9BYN7

Diamond homologs: A0JPL0, A2A761, A3KN32, A3KN36, A6NFI3, A6NM28, A6QLU5, A6QPT6, A7MBI1, A8MTY0, B2RXC5, B4DU55, E9PYI1, O14978, O60765, O75467, O75820, O95780, P0C7X2, P0DKX0, P0DPD5, P10072, P15622, P16374, P17014, P17023, P17032, P17098, P51523, P51786, P52738, P52742, Q02975, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q14590, Q14929, Q29RZ4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 56 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	8	30.8×	7e-09
Viral mRNA Translation	8	30.8×	7e-09
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	8	30.4×	7e-09
Selenocysteine synthesis	8	29.1×	7e-09
Eukaryotic Translation Termination	8	29.1×	7e-09
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	8	28.5×	7e-09
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	8	28.5×	7e-09
Formation of a pool of free 40S subunits	8	27.1×	9e-09

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	8	29.1×	8e-08
rRNA processing	5	13.9×	3e-03
translation	6	12.1×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1227 predictions. Top by Δscore:

Variant	Effect	Δscore
7:6642763:GG:G	donor_gain	1.0000
7:6642764:GG:G	donor_gain	1.0000
7:6642962:A:AG	acceptor_gain	1.0000
7:6642962:AG:A	acceptor_gain	1.0000
7:6642963:G:GA	acceptor_gain	1.0000
7:6642963:GG:G	acceptor_gain	1.0000
7:6642963:GGC:G	acceptor_gain	1.0000
7:6642963:GGCC:G	acceptor_gain	1.0000
7:6642963:GGCCT:G	acceptor_gain	1.0000
7:6643068:TGTC:T	donor_gain	1.0000
7:6643074:G:C	donor_loss	1.0000
7:6643820:A:AG	acceptor_gain	1.0000
7:6643820:AG:A	acceptor_gain	1.0000
7:6643821:G:GT	acceptor_gain	1.0000
7:6643821:GG:G	acceptor_gain	1.0000
7:6643821:GGA:G	acceptor_gain	1.0000
7:6643821:GGAGC:G	acceptor_gain	1.0000
7:6643909:G:GT	donor_gain	1.0000
7:6643909:G:T	donor_gain	1.0000
7:6643921:G:GT	donor_gain	1.0000
7:6643947:GG:G	donor_gain	1.0000
7:6643948:GG:G	donor_gain	1.0000
7:6643949:G:GG	donor_gain	1.0000
7:6643949:GTA:G	donor_loss	1.0000
7:6644474:T:A	acceptor_gain	1.0000
7:6644475:GGCA:G	acceptor_loss	1.0000
7:6644476:GCAG:G	acceptor_loss	1.0000
7:6644478:A:AG	acceptor_gain	1.0000
7:6644478:A:G	acceptor_loss	1.0000
7:6644478:AG:A	acceptor_gain	1.0000

AlphaMissense

6474 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:6652740:T:C	F382L	1.000
7:6652742:C:A	F382L	1.000
7:6652742:C:G	F382L	1.000
7:6652803:T:C	C403R	1.000
7:6652824:T:C	F410L	1.000
7:6652825:T:C	F410S	1.000
7:6652826:C:A	F410L	1.000
7:6652826:C:G	F410L	1.000
7:6653778:T:C	F728L	1.000
7:6653780:C:A	F728L	1.000
7:6653780:C:G	F728L	1.000
7:6654030:T:C	F812L	1.000
7:6654032:C:A	F812L	1.000
7:6654032:C:G	F812L	1.000
7:6654114:T:C	F840L	1.000
7:6654116:C:A	F840L	1.000
7:6654116:C:G	F840L	1.000
7:6654198:T:C	F868L	1.000
7:6654200:C:A	F868L	1.000
7:6654200:C:G	F868L	1.000
7:6654282:T:C	F896L	1.000
7:6654283:T:C	F896S	1.000
7:6654284:T:A	F896L	1.000
7:6654284:T:G	F896L	1.000
7:6654309:C:G	H905D	1.000
7:6654366:T:C	F924L	1.000
7:6654367:T:C	F924S	1.000
7:6654368:C:A	F924L	1.000
7:6654368:C:G	F924L	1.000
7:6652741:T:C	F382S	0.999

dbSNP variants (sampled 300 via entrez): RS1000187747 (7:6648682 CCAGA>C), RS1000220171 (7:6650299 C>G,T), RS1000267950 (7:6641460 G>C), RS1000344458 (7:6650509 G>A), RS1000519321 (7:6646289 G>T), RS1000635205 (7:6646533 C>T), RS1000780666 (7:6656556 A>G), RS1000860873 (7:6650688 A>T), RS1000868594 (7:6642622 G>A), RS1000913354 (7:6636370 C>A,T), RS1000944459 (7:6637222 C>A,G), RS1000966813 (7:6636587 C>G), RS1001104542 (7:6641437 C>A,G,T), RS1001195295 (7:6648076 T>C), RS1001320833 (7:6643624 TTTGAGC>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression, affects expression	3
Particulate Matter	increases abundance, increases expression	2
afuresertib	decreases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
coumarin	affects phosphorylation	1
pentanal	increases expression	1
abrine	increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	increases phosphorylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Methapyrilene	decreases methylation	1
Ozone	affects expression, increases abundance	1
Quercetin	decreases phosphorylation	1
Smoke	decreases expression	1
Thiram	increases expression	1
Cadmium Chloride	increases abundance, increases expression	1

Clinical trials (associated diseases)

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