ZNF506

Summary

ZNF506 (zinc finger protein 506, HGNC:23780) is a protein-coding gene on chromosome 19p13.11, encoding Zinc finger protein 506 (Q5JVG8). 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. Located in nucleolus.

Source: NCBI Gene 440515 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_001099269

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23780
Approved symbol	ZNF506
Name	zinc finger protein 506
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761G1812
Ensembl gene	ENSG00000081665
Ensembl biotype	protein_coding
Entrez	440515

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 7 protein_coding, 4 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000450683, ENST00000540806, ENST00000545006, ENST00000586260, ENST00000587452, ENST00000587461, ENST00000587822, ENST00000590274, ENST00000590319, ENST00000590766, ENST00000591639, ENST00000595825, ENST00000715984, ENST00000715985

RefSeq mRNA: 2 — MANE Select: NM_001099269 NM_001099269, NM_001145404

CCDS: CCDS42531, CCDS46027

Canonical transcript exons

ENST00000540806 — 4 exons

Exon	Start	End
ENSE00002858561	19821601	19821750
ENSE00003842956	19792711	19795660
ENSE00004028521	19806942	19807068
ENSE00004028523	19806031	19806126

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 91.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3907 / max 401.9012, expressed in 1614 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180170	21.3959	1609
180171	0.9949	600

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	91.83	gold quality
calcaneal tendon	UBERON:0003701	91.27	gold quality
tendon of biceps brachii	UBERON:0008188	89.06	gold quality
adrenal tissue	UBERON:0018303	88.88	gold quality
corpus callosum	UBERON:0002336	88.66	gold quality
cortical plate	UBERON:0005343	88.43	gold quality
tendon	UBERON:0000043	88.17	gold quality
buccal mucosa cell	CL:0002336	87.80	silver quality
sural nerve	UBERON:0015488	87.13	gold quality
caudate nucleus	UBERON:0001873	87.11	gold quality
nucleus accumbens	UBERON:0001882	87.00	gold quality
cerebellar cortex	UBERON:0002129	86.85	gold quality
cerebellar hemisphere	UBERON:0002245	86.84	gold quality
ganglionic eminence	UBERON:0004023	86.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.40	gold quality
thyroid gland	UBERON:0002046	86.40	gold quality
putamen	UBERON:0001874	86.32	gold quality
right lobe of thyroid gland	UBERON:0001119	86.27	gold quality
lower esophagus mucosa	UBERON:0035834	86.20	gold quality
left lobe of thyroid gland	UBERON:0001120	86.14	gold quality
lymph node	UBERON:0000029	85.98	gold quality
endometrium	UBERON:0001295	85.95	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.95	gold quality
cerebellum	UBERON:0002037	85.84	gold quality
right uterine tube	UBERON:0001302	85.58	gold quality
adenohypophysis	UBERON:0002196	85.48	gold quality
islet of Langerhans	UBERON:0000006	85.16	gold quality
left ovary	UBERON:0002119	85.13	gold quality
amygdala	UBERON:0001876	84.77	gold quality
anterior cingulate cortex	UBERON:0009835	84.72	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-110499	yes	138.29
E-ANND-3	yes	5.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

106 targeting ZNF506, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
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-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502

Literature-anchored findings (GeneRIF, showing 2)

• ZNF506-dependent positive feedback loop regulates H2AX signaling after DNA damage. (PMID:30013081)
• Unraveling the role of ZNF506 as a human PBS-pro-targeting protein for ERVP repression. (PMID:37697430)

Cross-species orthologs

0 orthologs

Paralogs (176): ZNF195 (ENSG00000005801), ZNF112 (ENSG00000062370), ZNF275 (ENSG00000063587), ZNF37A (ENSG00000075407), ZNF510 (ENSG00000081386), 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), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 506 — Q5JVG8 (reviewed: Q5JVG8)

All UniProt accessions (7): Q5JVG8, F5H490, K7EIG2, K7EIP5, K7ENQ3, K7ERD0, K7ERD9

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.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5JVG8-1	1	yes
Q5JVG8-2	2

RefSeq proteins (2): NP_001092739, NP_001138876 (=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, PF13912

UniProt features (13 total): zinc finger region 8, chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JVG8-F1	67.39	0.16

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 81 (showing top): GOZGIT_ESR1_TARGETS_DN, GARY_CD5_TARGETS_DN, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, OSMAN_BLADDER_CANCER_DN, GOCC_NUCLEOLUS, chr19p13, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, JOHNSTONE_PARVB_TARGETS_3_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, CHAF1B_TARGET_GENES, ZNF331_TARGET_GENES, ZNF350_TARGET_GENES, ZNF362_TARGET_GENES, ZNF711_TARGET_GENES, MIR153_5P

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

GO Molecular Function (5): 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), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleolus (GO:0005730), 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
cation binding	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

410 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF506	TMEM54	Q969K7	370
ZNF506	EYA3	Q99504	369
ZNF506	PRKRIP1	Q9H875	357
ZNF506	WBP2NL	Q6ICG8	349
ZNF506	AKR1B15	C9JRZ8	322
ZNF506	ST8SIA5	O15466	307
ZNF506	L3MBTL2	Q969R5	284
ZNF506	WDR97	A6NE52	280
ZNF506	KCTD10	Q9H3F6	278
ZNF506	XKR6	Q5GH73	271
ZNF506	PCDHA6	Q9UN73	271
ZNF506	ZPR1	O75312	263
ZNF506	IMPA2	O14732	251
ZNF506	ANKRD62	A6NC57	248
ZNF506	DGKI	O75912	247

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZNF506	ECE1	psi-mi:“MI:0915”(physical association)	0.370
ECE1	ZNF506	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (4): ZNF506 (Affinity Capture-RNA), ZNF506 (Affinity Capture-MS), ZNF506 (Affinity Capture-RNA), ZNF506 (Co-localization)

ESM2 similar proteins: A6NK75, A6NNF4, A6NP11, A8MTY0, A8MUV8, B4DX44, B4DXR9, O75346, O75373, O95780, P0CJ79, P0DKX0, P0DPD5, P17019, P17035, P35789, Q02386, Q03923, Q03938, Q14593, Q15928, Q2M3X9, Q3SXZ3, Q5JVG8, Q5RER9, Q68DY1, Q6JLC9, Q6PDB4, Q6ZMV8, Q6ZN06, Q6ZN08, Q86V71, Q8IW36, Q8IYN0, Q8N7M2, Q8NEM1, Q8NEP9, Q8TB69, Q8TD23, 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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

792 predictions. Top by Δscore:

Variant	Effect	Δscore
19:19806929:A:AC	donor_gain	1.0000
19:19806930:A:C	donor_gain	1.0000
19:19795656:CATAA:C	acceptor_gain	0.9900
19:19806925:A:AC	donor_gain	0.9900
19:19806926:C:CC	donor_gain	0.9900
19:19806981:C:A	donor_gain	0.9900
19:19807067:CC:C	acceptor_gain	0.9900
19:19807068:CC:C	acceptor_gain	0.9900
19:19807069:C:CC	acceptor_gain	0.9900
19:19821568:C:CA	donor_gain	0.9900
19:19806934:AT:A	donor_gain	0.9800
19:19806937:CTCAC:C	donor_loss	0.9800
19:19806938:TCACC:T	donor_loss	0.9800
19:19806940:ACCAA:A	donor_loss	0.9800
19:19806941:CCAA:C	donor_loss	0.9800
19:19807070:T:C	acceptor_loss	0.9800
19:19799594:CA:C	donor_gain	0.9700
19:19806940:A:AC	donor_gain	0.9700
19:19806941:C:CC	donor_gain	0.9700
19:19807066:TCC:T	acceptor_gain	0.9700
19:19807067:CCC:C	acceptor_gain	0.9700
19:19795658:TAA:T	acceptor_gain	0.9600
19:19795661:C:CC	acceptor_gain	0.9600
19:19806980:T:TA	donor_gain	0.9600
19:19807064:GGTCC:G	acceptor_gain	0.9600
19:19819609:CA:C	donor_gain	0.9600
19:19821595:TCTCA:T	donor_loss	0.9600
19:19821596:CTCA:C	donor_loss	0.9600
19:19821597:TCA:T	donor_loss	0.9600
19:19821598:CACC:C	donor_loss	0.9600

AlphaMissense

2946 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:19794921:A:C	F322L	0.996
19:19794921:A:T	F322L	0.996
19:19794923:A:G	F322L	0.996
19:19794753:A:C	F378L	0.995
19:19794753:A:T	F378L	0.995
19:19794755:A:G	F378L	0.995
19:19794669:A:C	F406L	0.993
19:19794669:A:T	F406L	0.993
19:19794671:A:G	F406L	0.993
19:19794837:A:C	F350L	0.993
19:19794837:A:T	F350L	0.993
19:19794839:A:G	F350L	0.993
19:19794916:C:G	R324P	0.991
19:19795005:A:C	F294L	0.990
19:19795005:A:T	F294L	0.990
19:19795007:A:G	F294L	0.990
19:19795089:A:C	F266L	0.988
19:19795089:A:T	F266L	0.988
19:19795091:A:G	F266L	0.988
19:19794904:A:G	L328P	0.982
19:19794894:A:C	H331Q	0.978
19:19794894:A:T	H331Q	0.978
19:19794922:A:G	F322S	0.973
19:19795001:A:G	S296P	0.973
19:19794754:A:G	F378S	0.972
19:19794820:A:G	L356P	0.972
19:19794966:A:C	H307Q	0.970
19:19794966:A:T	H307Q	0.970
19:19794988:A:G	L300P	0.970
19:19794896:G:C	H331D	0.968

dbSNP variants (sampled 300 via entrez): RS1000047772 (19:19793149 C>T), RS1000127439 (19:19807661 T>C,G), RS1000170710 (19:19798439 G>A,C), RS1000221153 (19:19801143 A>C,G), RS1000276011 (19:19823587 G>A), RS1000294574 (19:19801325 C>T), RS1000364193 (19:19805284 CAA>C,CA,CAAA), RS1000440968 (19:19792851 G>C), RS1000595921 (19:19811637 G>A), RS1000627335 (19:19811401 G>A), RS1000799053 (19:19805022 T>C), RS1000881574 (19:19822535 A>G,T), RS1000897618 (19:19821877 T>A), RS1000929794 (19:19821735 G>A), RS1000938027 (19:19816427 A>G)

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

1 associations (top):

Study	Trait	p-value
GCST006427_20	Depression in smokers	4.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
sodium arsenite	affects expression, decreases expression	2
Cisplatin	affects cotreatment, increases expression	2
Formaldehyde	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol A	decreases methylation	1
cinnamaldehyde	increases expression	1
potassium chromate(VI)	increases expression	1
nickel sulfate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Lead	increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	decreases methylation	1
Vanadates	decreases expression	1
Aflatoxin B1	increases expression	1
Asbestos, Serpentine	decreases methylation	1

Clinical trials (associated diseases)

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