ZNF479

Summary

ZNF479 (zinc finger protein 479, HGNC:23258) is a protein-coding gene on chromosome 7p11.2, encoding Zinc finger protein 479 (Q96JC4). 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 DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 90827 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 88 total
• MANE Select transcript: NM_001370129

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23258
Approved symbol	ZNF479
Name	zinc finger protein 479
Location	7p11.2
Locus type	gene with protein product
Status	Approved
Aliases	KR19
Ensembl gene	ENSG00000185177
Ensembl biotype	protein_coding
OMIM	617444
Entrez	90827

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000319636, ENST00000331162

RefSeq mRNA: 2 — MANE Select: NM_001370129 NM_001370129, NM_033273

CCDS: CCDS43590

Canonical transcript exons

ENST00000319636 — 4 exons

Exon	Start	End
ENSE00001260009	57117676	57121152
ENSE00001635697	57126018	57126113
ENSE00001727222	57126592	57126718
ENSE00003720002	57132286	57132436

Expression profiles

Bgee: expression breadth broad, 11 present calls, max score 88.41.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0123 / max 4.7248, expressed in 8 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
204454	0.0123	8

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	88.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.32	gold quality
right testis	UBERON:0004534	58.16	gold quality
left testis	UBERON:0004533	57.55	gold quality
testis	UBERON:0000473	57.48	gold quality
mucosa of paranasal sinus	UBERON:0005030	57.43	gold quality
lower lobe of lung	UBERON:0008949	56.85	silver quality
biceps brachii	UBERON:0001507	53.04	gold quality
lateral nuclear group of thalamus	UBERON:0002736	51.64	silver quality
tibia	UBERON:0000979	50.13	gold quality
tendon of biceps brachii	UBERON:0008188	49.01	gold quality
germinal epithelium of ovary	UBERON:0001304	47.65	gold quality
upper leg skin	UBERON:0004262	47.62	silver quality
vastus lateralis	UBERON:0001379	47.13	gold quality
quadriceps femoris	UBERON:0001377	46.97	gold quality
medial globus pallidus	UBERON:0002477	43.97	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
pigmented layer of retina	UBERON:0001782	42.53	gold quality
epithelium of nasopharynx	UBERON:0001951	42.30	gold quality
palpebral conjunctiva	UBERON:0001812	41.83	gold quality
subthalamic nucleus	UBERON:0001906	41.61	gold quality
substantia nigra pars compacta	UBERON:0001965	41.60	silver quality
inferior vagus X ganglion	UBERON:0005363	41.50	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
bronchial epithelial cell	CL:0002328	40.54	gold quality
bronchus	UBERON:0002185	40.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting ZNF479, 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-4262	100.00	73.26	3931
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-10393-5P	99.65	68.01	1368
HSA-MIR-142-3P	99.62	71.30	974
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-199A-5P	99.51	69.71	1107
HSA-MIR-199B-5P	99.51	69.74	1098
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-329-5P	99.27	68.11	1597
HSA-MIR-296-3P	99.21	66.56	474
HSA-MIR-6768-3P	99.14	67.38	1319
HSA-MIR-4464	98.95	67.73	820
HSA-MIR-4748	98.95	67.53	810
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-519A-2-5P	98.78	71.74	1401
HSA-MIR-520B-5P	98.78	71.74	1401
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-4684-5P	98.29	67.99	1650

Literature-anchored findings (GeneRIF, showing 2)

• ZNF479 regulates metallothionein-1 expression by modulating ASH2L in hepatocellular carcinoma. (PMID:31138789)
• Knockdown of ZNF479 inhibits proliferation and glycolysis of gastric cancer cells through regulating beta-catenin/c-Myc signaling pathway. (PMID:34042257)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000099025

Paralogs (18): ZNF430 (ENSG00000118620), ZNF92 (ENSG00000146757), ZNF66 (ENSG00000160229), ZNF22 (ENSG00000165512), ZNF680 (ENSG00000173041), ZNF114 (ENSG00000178150), ZFP41 (ENSG00000181638), ZNF730 (ENSG00000183850), ZNF626 (ENSG00000188171), ZNF431 (ENSG00000196705), ZNF100 (ENSG00000197020), ZNF257 (ENSG00000197134), ZNF98 (ENSG00000197360), ZNF675 (ENSG00000197372), ZNF273 (ENSG00000198039), ZNF737 (ENSG00000237440), ZNF253 (ENSG00000256771), ZNF723 (ENSG00000268696)

Protein

Protein identifiers

Zinc finger protein 479 — Q96JC4 (reviewed: Q96JC4)

Alternative names: Zinc finger protein Kr19

All UniProt accessions (1): Q96JC4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Expressed primarily in testis and fetal tissues.

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

RefSeq proteins (2): NP_001357058, NP_150376 (=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
IPR050758	Znf_C2H2-type	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-Q96JC4-F1	74.33	0.45

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 32 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR4262, MIR6809_3P, MIR181A_5P_MIR181B_5P, MIR181D_5P, MIR181C_5P, MIR3924, MIR519A_2_5P_MIR520B_5P, MIR4684_5P, MIR142_3P, GSE11057_EFF_MEM_VS_CENT_MEM_CD4_TCELL_DN, MIR199A_5P, MIR199B_5P, MIR4701_5P

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

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-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	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

308 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF479	BOD1L2	Q8IYS8	424
ZNF479	K7N7A8	K7N7A8	336
ZNF479	PAFAH1B3	Q15102	316
ZNF479	POM121L12	Q8N7R1	314
ZNF479	PPEF2	O14830	272
ZNF479	PPP1R3F	Q6ZSY5	271
ZNF479	SUMF2	Q8NBJ7	253
ZNF479	GON4L	Q3T8J9	251
ZNF479	RANBP6	O60518	249
ZNF479	IQSEC3	Q9UPP2	249
ZNF479	ZNHIT2	Q9UHR6	248
ZNF479	PTPRT	O14522	248
ZNF479	SMARCAD1	Q9H4L7	248
ZNF479	MT1H	P80294	246
ZNF479	GRXCR1	A8MXD5	246

IntAct

20 interactions, top by confidence:

A	B	Type	Score
KRTAP10-6	ZNF479	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF479	psi-mi:“MI:0915”(physical association)	0.560
ZNF479	MDFI	psi-mi:“MI:0915”(physical association)	0.560
KRTAP5-7	ZNF479	psi-mi:“MI:0915”(physical association)	0.560
STX1A	ZNF479	psi-mi:“MI:0915”(physical association)	0.560
BRAP	ZNF479	psi-mi:“MI:0915”(physical association)	0.370
ZNF254	TRIM24	psi-mi:“MI:0914”(association)	0.350
ZNF479	IPO8	psi-mi:“MI:0914”(association)	0.350
ZNF479	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
ZNF479	KRTAP5-7	psi-mi:“MI:0915”(physical association)	0.000
ZNF479	STX1A	psi-mi:“MI:0915”(physical association)	0.000
ZNF479	GOLGA6L9	psi-mi:“MI:0915”(physical association)	0.000
ZNF479	MDFI	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (8): ZNF479 (Two-hybrid), ZNF479 (Affinity Capture-MS), ZNF479 (Two-hybrid), ZNF479 (Two-hybrid), KRTAP10-6 (Two-hybrid), GOLGA6L9 (Two-hybrid), KRTAP5-7 (Two-hybrid), ZNF479 (Affinity Capture-MS)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0A1W2PQL4, A6NK75, A6NN14, A6NNF4, A6NP11, A8MQ14, A8MTY0, A8MUV8, A8MXY4, B4DX44, B4DXR9, E9PYI1, O14628, O43345, O75290, O75346, O75373, O75437, O95780, P0CB33, P0DKX0, P0DPD5, P16373, P17019, P17038, P21506, P35789, P52736, P52738, P52744, Q03923, Q03924, Q03936, Q03938, Q05481, Q14586, Q14593, Q14929, Q15928, Q3KNS6

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	83
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

955 predictions. Top by Δscore:

Variant	Effect	Δscore
7:57121153:C:CC	acceptor_gain	1.0000
7:57125788:CA:C	donor_gain	1.0000
7:57126575:A:AC	donor_gain	1.0000
7:57126576:C:CC	donor_gain	1.0000
7:57126587:CTCA:C	donor_loss	1.0000
7:57126588:TCACC:T	donor_loss	1.0000
7:57126589:CAC:C	donor_loss	1.0000
7:57126590:AC:A	donor_gain	1.0000
7:57126591:CC:C	donor_gain	1.0000
7:57126715:GTCC:G	acceptor_gain	1.0000
7:57126717:CC:C	acceptor_gain	1.0000
7:57126718:CC:C	acceptor_gain	1.0000
7:57126719:C:CC	acceptor_gain	1.0000
7:57126720:T:A	acceptor_loss	1.0000
7:57121148:CGTAA:C	acceptor_gain	0.9900
7:57121149:GTAA:G	acceptor_gain	0.9900
7:57121150:TAA:T	acceptor_gain	0.9900
7:57121151:AACTG:A	acceptor_loss	0.9900
7:57121152:ACT:A	acceptor_loss	0.9900
7:57121153:CTGAA:C	acceptor_loss	0.9900
7:57121154:T:G	acceptor_loss	0.9900
7:57126013:CCTA:C	donor_loss	0.9900
7:57126015:TA:T	donor_loss	0.9900
7:57126016:ACC:A	donor_loss	0.9900
7:57126110:ATACC:A	acceptor_loss	0.9900
7:57126111:TAC:T	acceptor_gain	0.9900
7:57126114:C:CA	acceptor_loss	0.9900
7:57126115:T:A	acceptor_loss	0.9900
7:57126122:T:TC	acceptor_gain	0.9900
7:57126584:AT:A	donor_gain	0.9900

AlphaMissense

3471 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:57120077:A:C	F446L	0.995
7:57120077:A:T	F446L	0.995
7:57120079:A:G	F446L	0.995
7:57119993:A:C	F474L	0.994
7:57119993:A:T	F474L	0.994
7:57119995:A:G	F474L	0.994
7:57120329:A:C	F362L	0.991
7:57120329:A:T	F362L	0.991
7:57120331:A:G	F362L	0.991
7:57120497:A:C	F306L	0.991
7:57120497:A:T	F306L	0.991
7:57120499:A:G	F306L	0.991
7:57120581:A:C	F278L	0.990
7:57120581:A:T	F278L	0.990
7:57120583:A:G	F278L	0.990
7:57120161:A:C	F418L	0.988
7:57120161:A:T	F418L	0.988
7:57120163:A:G	F418L	0.988
7:57120413:A:C	F334L	0.988
7:57120413:A:T	F334L	0.988
7:57120415:A:G	F334L	0.988
7:57119909:A:C	F502L	0.986
7:57119909:A:T	F502L	0.986
7:57119911:A:G	F502L	0.986
7:57120665:A:C	F250L	0.986
7:57120665:A:T	F250L	0.986
7:57120667:A:G	F250L	0.986
7:57120245:A:C	F390L	0.981
7:57120245:A:T	F390L	0.981
7:57120247:A:G	F390L	0.981

dbSNP variants (sampled 300 via entrez): RS1000043548 (7:57128487 C>T), RS1000325107 (7:57133592 C>A,T), RS1000335716 (7:57140219 T>C,G), RS1000371314 (7:57138605 A>G), RS1000696168 (7:57137619 T>C), RS1000706084 (7:57137341 GA>G,GAA), RS1000808545 (7:57127059 G>T), RS1001196973 (7:57132899 A>T), RS1001314419 (7:57127639 T>C), RS1001826428 (7:57133158 G>A), RS1002011930 (7:57139158 C>A,T), RS1002267601 (7:57127924 T>G), RS1002403643 (7:57139440 C>T), RS1002465964 (7:57138883 T>C), RS1002607852 (7:57126194 A>G)

Disease associations

OMIM: gene MIM:617444 | 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

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	decreases phosphorylation	1
bisphenol A	increases methylation	1
pentanal	decreases expression	1
CGP 52608	increases reaction, affects binding	1
bazedoxifene	increases expression	1
Resveratrol	affects cotreatment, decreases expression, increases expression	1
Air Pollutants	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, decreases expression, increases expression	1

Clinical trials (associated diseases)

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