ZNF415

Summary

ZNF415 (zinc finger protein 415, HGNC:20636) is a protein-coding gene on chromosome 19q13.42, encoding Zinc finger protein 415 (Q09FC8). 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 transcription by RNA polymerase II. Located in fibrillar center and microtubule cytoskeleton.

Source: NCBI Gene 55786 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 103 total
• MANE Select transcript: NM_018355

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20636
Approved symbol	ZNF415
Name	zinc finger protein 415
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000170954
Ensembl biotype	protein_coding
OMIM	619506
Entrez	55786

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 20 protein_coding, 6 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000243643, ENST00000421033, ENST00000500065, ENST00000594011, ENST00000594286, ENST00000595174, ENST00000595193, ENST00000595359, ENST00000595813, ENST00000596051, ENST00000596106, ENST00000596683, ENST00000597503, ENST00000597748, ENST00000597877, ENST00000598024, ENST00000598578, ENST00000599261, ENST00000600098, ENST00000600120, ENST00000600574, ENST00000601110, ENST00000601215, ENST00000601493, ENST00000602024, ENST00000602110, ENST00000882509, ENST00000882510, ENST00000937691, ENST00000937692, ENST00000937693

RefSeq mRNA: 26 — MANE Select: NM_018355 NM_001136038, NM_001164309, NM_001330759, NM_001330766, NM_001352130, NM_001352131, NM_001352132, NM_001352133, NM_001352134, NM_001352135, NM_001352136, NM_001352137, NM_001352138, NM_001352139, NM_001352140, NM_001352141, NM_001352142, NM_001352143, NM_001352144, NM_001352146, NM_001352147, NM_001352148, NM_001352149, NM_001352150, NM_001352151, NM_018355

CCDS: CCDS12860, CCDS54313, CCDS82393

Canonical transcript exons

ENST00000243643 — 4 exons

Exon	Start	End
ENSE00003510836	53122662	53122743
ENSE00003583694	53107879	53109908
ENSE00003733178	53116313	53116433
ENSE00003921462	53132856	53132910

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 95.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9561 / max 110.6103, expressed in 924 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182553	3.9359	924
182552	0.0146	3
182551	0.0056	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	95.22	gold quality
male germ cell	CL:0000015	93.40	gold quality
adrenal tissue	UBERON:0018303	92.21	gold quality
cortical plate	UBERON:0005343	90.64	gold quality
right adrenal gland cortex	UBERON:0035827	89.09	gold quality
right adrenal gland	UBERON:0001233	88.90	gold quality
left adrenal gland	UBERON:0001234	88.72	gold quality
right testis	UBERON:0004534	88.59	gold quality
left testis	UBERON:0004533	88.53	gold quality
left adrenal gland cortex	UBERON:0035825	88.49	gold quality
cerebellar hemisphere	UBERON:0002245	88.20	gold quality
cerebellar cortex	UBERON:0002129	88.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.90	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.81	gold quality
adrenal gland	UBERON:0002369	87.68	gold quality
adrenal cortex	UBERON:0001235	87.59	gold quality
testis	UBERON:0000473	87.57	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.82	gold quality
cerebellum	UBERON:0002037	86.60	gold quality
prefrontal cortex	UBERON:0000451	85.69	gold quality
ganglionic eminence	UBERON:0004023	85.64	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.22	gold quality
right frontal lobe	UBERON:0002810	85.20	gold quality
spinal cord	UBERON:0002240	84.96	gold quality
corpus callosum	UBERON:0002336	84.76	gold quality
right atrium auricular region	UBERON:0006631	84.34	gold quality
heart left ventricle	UBERON:0002084	84.20	gold quality
amygdala	UBERON:0001876	84.06	gold quality
putamen	UBERON:0001874	84.03	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.96	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting ZNF415, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-1277-5P	100.00	73.95	5056
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-5011-5P	100.00	83.46	5820
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-4764-5P	98.88	65.53	894
HSA-MIR-4439	98.53	67.53	793
HSA-MIR-3136-5P	98.53	67.68	793
HSA-MIR-8078	98.32	65.73	361
HSA-MIR-6818-5P	97.50	67.10	1167
HSA-MIR-96-3P	97.47	68.03	839
HSA-MIR-4433B-3P	97.22	63.62	663

Literature-anchored findings (GeneRIF, showing 2)

• ZNF415 isoforms in COS-7 cells inhibits the transcriptional activities of AP-1 and p53, suggesting that the ZNF415 protein may be involved in AP-1- and p53-mediated transcriptional activity. (PMID:17055453)
• ZfLp is a zinc finger protein that functions as a drug carrier protein. (PMID:22863851)

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 415 — Q09FC8 (reviewed: Q09FC8)

All UniProt accessions (12): Q09FC8, M0QX59, M0QXZ4, M0QZ38, M0QZA6, M0R0D9, M0R0R1, M0R191, M0R1N1, M0R2I1, M0R2T6, M0R358

UniProt curated annotations — full annotation on UniProt →

Function. Involved in transcriptional regulation. Transcriptional activity differed among the various isoforms. All isoforms except isoform 3 seem to suppresses the transcriptional activities of AP-1 and p53/TP53.

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Expressed in all tissues examined. Isoforms are differentially expressed. Isoform 3 and isoform 5 were highly expressed, isoform 4 moderately expressed, isoform 2 lower expression, the lowest expression level was seem with isoform 1.

Isoforms (6)

UniProt ID	Names	Canonical?
Q09FC8-1	1, ZNF415-3	yes
Q09FC8-2	2, ZNF415-2
Q09FC8-3	3, ZNF415-1
Q09FC8-4	4, ZNF415-4
Q09FC8-5	5, ZNF415-5
Q09FC8-6	6

RefSeq proteins (26): NP_001129510, NP_001157781, NP_001317688, NP_001317695, NP_001339059, NP_001339060, NP_001339061, NP_001339062, NP_001339063, NP_001339064, NP_001339065, NP_001339066, NP_001339067, NP_001339068, NP_001339069, NP_001339070, NP_001339071, NP_001339072, NP_001339073, NP_001339075, NP_001339076, NP_001339077, NP_001339078, NP_001339079, NP_001339080, NP_060825* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (23 total): zinc finger region 12, splice variant 5, sequence variant 5, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q09FC8-F1	58.95	0.23

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 56 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, BERENJENO_TRANSFORMED_BY_RHOA_UP, MARSON_BOUND_BY_E2F4_UNSTIMULATED, JAIN_NFKB_SIGNALING, GOCC_NUCLEOLUS, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_ICP_WITH_H3K4ME3, PEDRIOLI_MIR31_TARGETS_DN, ROESSLER_LIVER_CANCER_METASTASIS_DN, ONKEN_UVEAL_MELANOMA_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, P53_DN.V1_UP, PIEPOLI_LGI1_TARGETS_DN, SHEN_SMARCA2_TARGETS_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY

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

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 (5): fibrillar center (GO:0001650), nucleus (GO:0005634), cytoplasm (GO:0005737), microtubule cytoskeleton (GO:0015630), nucleolus (GO:0005730)

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
cellular anatomical structure	2
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
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
nucleolus	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoskeleton	1
nuclear lumen	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

376 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF415	ANHX	E9PGG2	419
ZNF415	LRATD1	Q96KN4	396
ZNF415	CALHM2	Q9HA72	389
ZNF415	MDFI	Q99750	356
ZNF415	LRRC70	Q7Z2Q7	348
ZNF415	ELOVL4	Q9GZR5	311
ZNF415	NBPF20	P0DPF2	302
ZNF415	CCDC59	Q9P031	296
ZNF415	CNTNAP2	Q9UHC6	288
ZNF415	RNF141	Q8WVD5	272
ZNF415	TMEM25	Q86YD3	270
ZNF415	KRT37	O76014	258
ZNF415	KRT38	O76015	252
ZNF415	ABHD3	Q8WU67	252
ZNF415	SOX14	O95416	252

IntAct

8 interactions, top by confidence:

A	B	Type	Score
MTUS2	ZNF415	psi-mi:“MI:0915”(physical association)	0.560
KRTAP4-12	ZNF415	psi-mi:“MI:0915”(physical association)	0.560
ZNF415	KRTAP4-12	psi-mi:“MI:0915”(physical association)	0.560
ZNF415	MTUS2	psi-mi:“MI:0915”(physical association)	0.560
M		psi-mi:“MI:0914”(association)	0.350

BioGRID (8): ZNF415 (Two-hybrid), KRTAP4-12 (Two-hybrid), ZNF415 (Synthetic Lethality), ZNF415 (Two-hybrid), ZNF415 (Affinity Capture-MS), ZNF415 (Negative Genetic), ZNF415 (Reconstituted Complex), ZNF415 (Two-hybrid)

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: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	88
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1027 predictions. Top by Δscore:

Variant	Effect	Δscore
19:53109904:CAGAT:C	acceptor_gain	1.0000
19:53109905:AGAT:A	acceptor_gain	1.0000
19:53109906:GAT:G	acceptor_gain	1.0000
19:53109907:AT:A	acceptor_gain	1.0000
19:53109907:ATCTA:A	acceptor_loss	1.0000
19:53109908:TC:T	acceptor_loss	1.0000
19:53109909:C:CC	acceptor_gain	1.0000
19:53109909:C:T	acceptor_loss	1.0000
19:53109911:A:C	acceptor_gain	1.0000
19:53109918:A:AC	acceptor_gain	1.0000
19:53109918:A:C	acceptor_gain	1.0000
19:53116439:C:CT	acceptor_gain	1.0000
19:53116439:C:T	acceptor_gain	1.0000
19:53109910:T:C	acceptor_loss	0.9900
19:53109911:A:AC	acceptor_gain	0.9900
19:53116434:C:CC	acceptor_gain	0.9900
19:53116440:G:C	acceptor_gain	0.9900
19:53122742:TG:T	acceptor_gain	0.9900
19:53122744:C:CC	acceptor_gain	0.9900
19:53132855:CG:C	donor_gain	0.9900
19:53116431:CAA:C	acceptor_gain	0.9800
19:53116440:G:GC	acceptor_gain	0.9800
19:53122739:CAATG:C	acceptor_gain	0.9800
19:53132854:A:AC	donor_gain	0.9800
19:53132855:C:CC	donor_gain	0.9800
19:53109907:ATCT:A	acceptor_gain	0.9700
19:53109908:TCTA:T	acceptor_gain	0.9700
19:53116311:AC:A	donor_gain	0.9700
19:53116312:CC:C	donor_gain	0.9700
19:53116352:C:A	donor_gain	0.9700

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000156017 (19:53121936 G>C), RS1000220764 (19:53118123 T>C), RS1000494431 (19:53122942 ACTCCCTC>A), RS1000568842 (19:53115074 G>A), RS1000599906 (19:53114791 G>A), RS1000703636 (19:53117551 T>C), RS1000801155 (19:53111331 A>G,T), RS1001226258 (19:53120299 A>C), RS1001407479 (19:53131033 T>C), RS1001452506 (19:53114224 T>C), RS1001481541 (19:53113997 C>T), RS1001567427 (19:53134104 A>G), RS1001656363 (19:53120076 A>T), RS1001752586 (19:53107559 A>G), RS1001776468 (19:53129078 T>A,G)

Disease associations

OMIM: gene MIM:619506 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	2
Nickel	decreases expression	2
Oxygen	decreases expression, increases expression	2
Valproic Acid	decreases expression	2
GSK-J4	decreases expression	1
arsenite	affects binding, increases reaction	1
aflatoxin B2	decreases methylation	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases expression	1
Decitabine	decreases expression, decreases reaction	1
Leflunomide	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Doxorubicin	decreases expression	1
Smoke	decreases expression, decreases reaction	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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