ZNF517

Summary

ZNF517 (zinc finger protein 517, HGNC:27984) is a protein-coding gene on chromosome 8q24.3, encoding Zinc finger protein 517 (Q6ZMY9). 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 340385 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 114 total
• MANE Select transcript: NM_213605

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27984
Approved symbol	ZNF517
Name	zinc finger protein 517
Location	8q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197363
Ensembl biotype	protein_coding
Entrez	340385

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000359971, ENST00000525105, ENST00000526178, ENST00000528012, ENST00000529429, ENST00000530879, ENST00000533965, ENST00000903326, ENST00000903327

RefSeq mRNA: 7 — MANE Select: NM_213605 NM_001317936, NM_001384904, NM_001384905, NM_001384906, NM_001384907, NM_001384908, NM_213605

CCDS: CCDS6434, CCDS94367

Canonical transcript exons

ENST00000359971 — 5 exons

Exon	Start	End
ENSE00001413398	144807191	144810084
ENSE00001422286	144803641	144803767
ENSE00003487853	144804125	144804238
ENSE00003505352	144802870	144802947
ENSE00003917455	144798913	144798937

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 84.26.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4943 / max 15.8044, expressed in 256 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
91536	0.4943	256

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	84.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	82.63	gold quality
cerebellar hemisphere	UBERON:0002245	82.33	gold quality
cerebellar cortex	UBERON:0002129	82.17	gold quality
right frontal lobe	UBERON:0002810	81.80	gold quality
left ovary	UBERON:0002119	81.64	gold quality
right ovary	UBERON:0002118	81.26	gold quality
body of uterus	UBERON:0009853	81.15	gold quality
right adrenal gland	UBERON:0001233	81.12	gold quality
ganglionic eminence	UBERON:0004023	80.97	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.94	gold quality
anterior cingulate cortex	UBERON:0009835	80.94	gold quality
Brodmann (1909) area 9	UBERON:0013540	80.75	gold quality
apex of heart	UBERON:0002098	80.74	gold quality
gastrocnemius	UBERON:0001388	80.67	gold quality
left adrenal gland	UBERON:0001234	80.59	gold quality
right adrenal gland cortex	UBERON:0035827	80.50	gold quality
left adrenal gland cortex	UBERON:0035825	80.45	gold quality
muscle of leg	UBERON:0001383	80.22	gold quality
prefrontal cortex	UBERON:0000451	80.15	gold quality
ventricular zone	UBERON:0003053	80.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.94	gold quality
left uterine tube	UBERON:0001303	79.62	gold quality
cerebellum	UBERON:0002037	79.40	gold quality
lower esophagus muscularis layer	UBERON:0035833	79.37	gold quality
lower esophagus	UBERON:0013473	79.36	gold quality
stromal cell of endometrium	CL:0002255	79.34	gold quality
adenohypophysis	UBERON:0002196	79.31	gold quality
lower esophagus mucosa	UBERON:0035834	79.31	gold quality
mucosa of stomach	UBERON:0001199	79.26	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting ZNF517, 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-6778-3P	99.96	67.29	2693
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-3674	97.01	68.86	1171
HSA-MIR-3690	96.44	65.18	737

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 517 — Q6ZMY9 (reviewed: Q6ZMY9)

All UniProt accessions (4): E9PIL1, Q6ZMY9, G3V191, H0YCN3

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 (7): NP_001304865, NP_001371833, NP_001371834, NP_001371835, NP_001371836, NP_001371837, NP_998770* (*=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
IPR050752	C2H2-ZF_domain	Family

Pfam: PF00096, PF01352

UniProt features (19 total): zinc finger region 10, region of interest 2, compositionally biased region 2, sequence conflict 2, chain 1, domain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZMY9-F1	68.77	0.01

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 20 (showing top): NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, chr8q24, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CHAF1B_TARGET_GENES, PAX7_TARGET_GENES, RBM34_TARGET_GENES, UBN1_TARGET_GENES, ZNF423_TARGET_GENES, DESCARTES_MAIN_FETAL_CLC_IL5RA_POSITIVE_CELLS, ZBED5_TARGET_GENES, ZNF579_TARGET_GENES, ADA2_TARGET_GENES, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_12H_ACT_CD4_TCELL_DN

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)

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
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

418 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF517	Q8N1N5	Q8N1N5	580
ZNF517	COMMD5	Q9GZQ3	530
ZNF517	ZNF385B	Q569K4	511
ZNF517	ZNF292	O60281	461
ZNF517	TSHZ3	Q63HK5	452
ZNF517	ZFPM1	Q8IX07	359
ZNF517	LRIG1	Q96JA1	348
ZNF517	DGKZ	Q13574	348
ZNF517	MPV17L2	Q567V2	348
ZNF517	TTK	P33981	330
ZNF517	POGZ	Q7Z3K3	322
ZNF517	MRFAP1L2	B2RBV5	322
ZNF517	ZBTB21	Q9ULJ3	310
ZNF517	SYAP1	Q96A49	303
ZNF517	KLHDC3	Q9BQ90	296

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF517	GGPS1	psi-mi:“MI:0914”(association)	0.530

BioGRID (46): NUDT12 (Affinity Capture-MS), NPHP3 (Affinity Capture-MS), MICAL1 (Affinity Capture-MS), LRP1B (Affinity Capture-MS), NDUFAF7 (Affinity Capture-MS), IPP (Affinity Capture-MS), ERBB2IP (Affinity Capture-MS), SORL1 (Affinity Capture-MS), PPP2R5E (Affinity Capture-MS), PPP2CA (Affinity Capture-MS), RNF41 (Affinity Capture-MS), GNB2 (Affinity Capture-MS), ACTBL2 (Affinity Capture-MS), EFR3A (Affinity Capture-MS), TRIM28 (Affinity Capture-MS)

ESM2 similar proteins: A2CE44, A6NFI3, A6NM28, A8K8V0, O15370, O70218, O95201, P0CJ78, P10075, P10754, P28698, P70338, Q04890, Q07120, Q14V87, Q19A40, Q569E7, Q58DK7, Q5DWN0, Q5FWU5, Q5RJR4, Q5T619, Q5TEC3, Q6DD87, Q6IQX8, Q6PD29, Q6PGE4, Q6ZMY9, Q7Z7K2, Q80VM4, Q8BIF9, Q8JZL0, Q8N8E2, Q8NAF0, Q8NCA9, Q8TD94, Q8WUU4, Q96C55, Q96H86, Q96MX3

Diamond homologs: A0JPL0, A1L1L7, A2A761, A2VDP4, A3KN36, A6QLU5, A6QPT6, A7MBI1, A8MT65, B2RXC5, E9PYI1, E9Q8G5, O75290, O94892, O95780, P10076, P17014, P17023, P17025, P17030, P17032, P17098, P51523, P51814, P52736, P52742, P58317, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14584, Q14587, Q14590, Q147U1, Q16587, Q29RZ4, Q2M218

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	106
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1149 predictions. Top by Δscore:

Variant	Effect	Δscore
8:144798936:GG:G	donor_gain	1.0000
8:144798937:GG:G	donor_gain	1.0000
8:144804236:CAGGT:C	donor_loss	1.0000
8:144804239:G:A	donor_loss	1.0000
8:144804240:T:A	donor_loss	1.0000
8:144798934:CAGGG:C	donor_loss	0.9900
8:144798936:GGGTG:G	donor_loss	0.9900
8:144798938:G:GG	donor_gain	0.9900
8:144798939:T:A	donor_loss	0.9900
8:144802868:A:AG	acceptor_gain	0.9900
8:144802869:G:GG	acceptor_gain	0.9900
8:144803589:T:A	acceptor_gain	0.9900
8:144803590:G:A	acceptor_gain	0.9900
8:144803764:CTAG:C	donor_loss	0.9900
8:144803766:AGGT:A	donor_loss	0.9900
8:144803767:GG:G	donor_loss	0.9900
8:144803768:G:GA	donor_loss	0.9900
8:144803769:T:G	donor_loss	0.9900
8:144804116:T:A	acceptor_gain	0.9900
8:144804144:A:AG	acceptor_gain	0.9900
8:144804145:G:GG	acceptor_gain	0.9900
8:144804237:AG:A	donor_gain	0.9900
8:144804238:GG:G	donor_gain	0.9900
8:144804239:G:GG	donor_gain	0.9900
8:144804241:GAG:G	donor_loss	0.9900
8:144807189:AGAT:A	acceptor_loss	0.9900
8:144798934:CAGG:C	donor_gain	0.9800
8:144798935:AGG:A	donor_gain	0.9800
8:144798936:GGG:G	donor_gain	0.9800
8:144802869:GA:G	acceptor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000065709 (8:144801787 T>A), RS1000100420 (8:144806074 T>C), RS1000154023 (8:144796956 C>G), RS1000164496 (8:144800981 C>T), RS1000621377 (8:144801206 C>A,T), RS1000901112 (8:144809577 C>G,T), RS1000963327 (8:144810021 C>T), RS1000970121 (8:144806138 T>G), RS1001012821 (8:144804785 C>T), RS1001028711 (8:144800895 G>A,C,T), RS1001102492 (8:144805048 T>C), RS1001192715 (8:144811108 C>A,T), RS1001353477 (8:144809778 G>A), RS1001455216 (8:144810586 G>A,C), RS1001469221 (8:144805576 G>A,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

2 associations (top):

Study	Trait	p-value
GCST007005_3	Logical memory (immediate recall) in normal cognition	5.000000e-07
GCST007005_4	Logical memory (immediate recall) in normal cognition	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004874	memory performance

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
aminomethylphosphonic acid (AMPA)	decreases expression	1
benzo(e)pyrene	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
jinfukang	increases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Cadmium	increases abundance, increases expression	1
Methapyrilene	decreases methylation	1
Smoke	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
2,4-Dichlorophenoxyacetic Acid	decreases expression	1
Palmitic Acid	increases expression	1

Clinical trials (associated diseases)

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