ZNF79

Summary

ZNF79 (zinc finger protein 79, HGNC:13153) is a protein-coding gene on chromosome 9q33.3, encoding Zinc finger protein 79 (Q15937). 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 7633 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 88 total
• MANE Select transcript: NM_007135

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13153
Approved symbol	ZNF79
Name	zinc finger protein 79
Location	9q33.3
Locus type	gene with protein product
Status	Approved
Aliases	pT7
Ensembl gene	ENSG00000196152
Ensembl biotype	protein_coding
OMIM	194552
Entrez	7633

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000342483, ENST00000543471, ENST00000612342, ENST00000617266, ENST00000850855, ENST00000850856, ENST00000850857

RefSeq mRNA: 5 — MANE Select: NM_007135 NM_001286696, NM_001286697, NM_001286698, NM_001322260, NM_007135

CCDS: CCDS6871, CCDS69664, CCDS75904

Canonical transcript exons

ENST00000342483 — 5 exons

Exon	Start	End
ENSE00001036799	127435908	127436003
ENSE00001036811	127435090	127435216
ENSE00001460343	127444029	127445372
ENSE00001460347	127424382	127424803
ENSE00003520666	127428832	127428920

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 84.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.1494 / max 91.3627, expressed in 1785 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98607	8.1494	1785

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.82	gold quality
tendon of biceps brachii	UBERON:0008188	84.47	gold quality
tendon	UBERON:0000043	77.95	gold quality
calcaneal tendon	UBERON:0003701	76.96	gold quality
granulocyte	CL:0000094	76.54	gold quality
stromal cell of endometrium	CL:0002255	76.24	gold quality
amniotic fluid	UBERON:0000173	75.73	gold quality
islet of Langerhans	UBERON:0000006	75.60	gold quality
medial globus pallidus	UBERON:0002477	75.23	gold quality
buccal mucosa cell	CL:0002336	75.09	silver quality
muscle of leg	UBERON:0001383	74.89	gold quality
secondary oocyte	CL:0000655	74.84	gold quality
gastrocnemius	UBERON:0001388	74.78	gold quality
hindlimb stylopod muscle	UBERON:0004252	74.44	gold quality
apex of heart	UBERON:0002098	73.83	gold quality
cortical plate	UBERON:0005343	73.74	gold quality
muscle organ	UBERON:0001630	73.66	gold quality
globus pallidus	UBERON:0001875	73.47	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.44	gold quality
ganglionic eminence	UBERON:0004023	72.84	gold quality
ventricular zone	UBERON:0003053	72.81	gold quality
right adrenal gland cortex	UBERON:0035827	72.71	gold quality
smooth muscle tissue	UBERON:0001135	72.64	gold quality
left adrenal gland	UBERON:0001234	72.64	gold quality
endothelial cell	CL:0000115	72.58	silver quality
leukocyte	CL:0000738	72.31	gold quality
right adrenal gland	UBERON:0001233	72.26	gold quality
adrenal gland	UBERON:0002369	72.17	gold quality
left adrenal gland cortex	UBERON:0035825	72.12	gold quality
monocyte	CL:0000576	72.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.84

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

2 targets.

Target	Regulation
CAT
TICAM2

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

8 targeting ZNF79, 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-498-5P	99.76	69.64	1807
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-4771	97.43	67.69	596
HSA-MIR-4785	88.53	62.71	63

Cross-species orthologs

0 orthologs

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZNF549 (ENSG00000121406), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 79 — Q15937 (reviewed: Q15937)

Alternative names: ZNFpT7

All UniProt accessions (3): Q15937, A0A087X2B0, F5H032

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 (5): NP_001273625, NP_001273626, NP_001273627, NP_001309189, NP_009066* (*=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
IPR050527

Pfam: PF00096

UniProt features (19 total): zinc finger region 11, sequence variant 3, sequence conflict 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15937-F1	68.95	0.44

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 57 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, MODULE_48, MODULE_95, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MARTENS_TRETINOIN_RESPONSE_DN, SMIRNOV_RESPONSE_TO_IR_6HR_UP, WARTERS_RESPONSE_TO_IR_SKIN, ZWANG_DOWN_BY_2ND_EGF_PULSE, MODULE_163, JNK_DN.V1_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, BANP_TARGET_GENES, CREB3L4_TARGET_GENES

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (7): 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), transcription cis-regulatory region binding (GO:0000976), 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
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
positive regulation of DNA-templated transcription	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
transition metal ion binding	1
transcription regulatory region nucleic acid binding	1
sequence-specific double-stranded DNA binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

526 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF79	COL5A1	P20908	752
ZNF79	OR2AG1	Q9H205	669
ZNF79	ACVRL1	P37023	590
ZNF79	ENG	P17813	587
ZNF79	BMPR2	Q13873	546
ZNF79	TFPI	P10646	542
ZNF79	Q6IQ01	Q6IQ01	469
ZNF79	ADCY10	Q96PN6	401
ZNF79	ZNF77	Q15935	391
ZNF79	DEF8	Q6ZN54	335
ZNF79	OR8G1	Q15617	320
ZNF79	RNF112	Q9ULX5	300
ZNF79	HSD17B10	Q99714	294
ZNF79	C11orf24	Q96F05	292
ZNF79	OR51F1	A6NGY5	287

IntAct

29 interactions, top by confidence:

A	B	Type	Score
ZNF79	TRIM27	psi-mi:“MI:0915”(physical association)	0.560
MDFI	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
ZNF79		psi-mi:“MI:0915”(physical association)	0.560
TRIM27	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
KRTAP10-8	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
KRT34	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
ZBTB24	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
FGF12	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
YJU2B	ZNF79	psi-mi:“MI:0915”(physical association)	0.560
ZNF79	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF79	KRTAP10-8	psi-mi:“MI:0915”(physical association)	0.000
ZNF79	KRTAP6-3	psi-mi:“MI:0915”(physical association)	0.000
ZNF79	KRT34	psi-mi:“MI:0915”(physical association)	0.000
FGF12	ZNF79	psi-mi:“MI:0915”(physical association)	0.000
ZBTB24	ZNF79	psi-mi:“MI:0915”(physical association)	0.000
ZNF79	YJU2B	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (13): ZNF79 (Two-hybrid), ZNF79 (Two-hybrid), KRTAP10-3 (Two-hybrid), ZNF79 (Affinity Capture-RNA), ZNF79 (Affinity Capture-RNA), ZNF79 (Affinity Capture-MS), ZNF79 (Two-hybrid), ZNF79 (Two-hybrid), ZNF79 (Two-hybrid), ZNF79 (Two-hybrid), ZNF79 (Two-hybrid), KRTAP6-3 (Two-hybrid), ZNF79 (Negative Genetic)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: B1H2Q6, G5EGB2, O15535, O75290, P17026, P18724, P18741, P18747, P52742, Q15937, Q17895, Q1LZC0, Q3MJ62, Q4R7X8, Q5R4X5, Q6A085, Q7Z3I7, Q8BGV5, Q8TBZ5, Q91VW9, Q969J2, Q9BRR0, Q9ERU2, Q9ERU3, Q9UEG4, Q9Z1D9, Q9Z2K3, A8MQ14, P17097, P21506, Q03936, Q29RZ4, Q3KNS6, Q3V080, Q5RBX0, Q5RBY9, Q5T619, Q6DD87, Q6J6I6, Q6PG37

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1295 predictions. Top by Δscore:

Variant	Effect	Δscore
9:127424671:G:GT	donor_gain	1.0000
9:127428830:A:AG	acceptor_gain	1.0000
9:127428831:G:GA	acceptor_gain	1.0000
9:127428831:GTA:G	acceptor_gain	1.0000
9:127428831:GTACT:G	acceptor_gain	1.0000
9:127435088:A:AG	acceptor_gain	1.0000
9:127435088:AG:A	acceptor_gain	1.0000
9:127435088:AGG:A	acceptor_gain	1.0000
9:127435089:G:A	acceptor_loss	1.0000
9:127435089:G:GG	acceptor_gain	1.0000
9:127435089:GG:G	acceptor_gain	1.0000
9:127435089:GGG:G	acceptor_gain	1.0000
9:127435191:A:T	donor_gain	1.0000
9:127435213:CTAGG:C	donor_loss	1.0000
9:127435214:TAGG:T	donor_loss	1.0000
9:127435215:AGG:A	donor_loss	1.0000
9:127435216:GGTA:G	donor_loss	1.0000
9:127435217:G:A	donor_loss	1.0000
9:127435218:T:G	donor_loss	1.0000
9:127435901:T:A	acceptor_gain	1.0000
9:127435905:TAG:T	acceptor_loss	1.0000
9:127435905:TAGGA:T	acceptor_gain	1.0000
9:127435906:A:AG	acceptor_gain	1.0000
9:127435906:A:AT	acceptor_loss	1.0000
9:127435906:AG:A	acceptor_gain	1.0000
9:127435907:G:GG	acceptor_gain	1.0000
9:127435907:GG:G	acceptor_gain	1.0000
9:127435907:GGA:G	acceptor_gain	1.0000
9:127435907:GGAC:G	acceptor_gain	1.0000
9:127436004:G:GC	donor_loss	1.0000

AlphaMissense

3318 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:127444892:T:C	F398L	0.999
9:127444894:C:A	F398L	0.999
9:127444894:C:G	F398L	0.999
9:127444388:T:C	F230L	0.998
9:127444390:C:A	F230L	0.998
9:127444390:C:G	F230L	0.998
9:127444472:T:C	F258L	0.998
9:127444474:C:A	F258L	0.998
9:127444474:C:G	F258L	0.998
9:127444556:T:C	F286L	0.998
9:127444558:C:A	F286L	0.998
9:127444558:C:G	F286L	0.998
9:127444640:T:C	F314L	0.998
9:127444642:C:A	F314L	0.998
9:127444642:C:G	F314L	0.998
9:127444808:T:C	F370L	0.998
9:127444810:C:A	F370L	0.998
9:127444810:C:G	F370L	0.998
9:127444827:T:C	L376P	0.998
9:127445060:T:C	F454L	0.998
9:127445062:T:A	F454L	0.998
9:127445062:T:G	F454L	0.998
9:127444506:G:C	R269P	0.997
9:127444724:T:C	F342L	0.997
9:127444726:C:A	F342L	0.997
9:127444726:C:G	F342L	0.997
9:127444837:T:A	H379Q	0.997
9:127444837:T:G	H379Q	0.997
9:127444911:T:C	L404P	0.997
9:127444304:T:C	F202L	0.996

dbSNP variants (sampled 300 via entrez): RS1000103421 (9:127444360 C>G,T), RS1000155790 (9:127444589 A>G), RS1000195555 (9:127426031 A>G), RS1000238705 (9:127438283 A>T), RS1000301393 (9:127431519 G>T), RS1000472875 (9:127424659 G>A), RS1000537730 (9:127443673 G>A,C), RS1000631037 (9:127426341 C>G), RS1000860296 (9:127436786 G>A,C), RS1000923222 (9:127431225 T>C), RS1000963194 (9:127424395 C>T), RS1001158167 (9:127443352 C>T), RS1001234325 (9:127424618 G>A), RS1001292640 (9:127437143 G>A), RS1001361136 (9:127430551 C>G,T)

Disease associations

OMIM: gene MIM:194552 | 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

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	6
Aflatoxin B1	increases expression, affects expression	3
sodium arsenite	increases expression, affects cotreatment, decreases expression, increases abundance	2
Formaldehyde	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
tobacco tar	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
cupric oxide	increases expression	1
resorcinol	decreases expression	1
polyhexamethyleneguanidine	affects expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	affects cotreatment, increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Camptothecin	increases expression	1
Cisplatin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects expression	1
Ethyl Methanesulfonate	increases expression	1

Clinical trials (associated diseases)

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