ZNF117

Summary

ZNF117 (zinc finger protein 117, HGNC:12897) is a protein-coding gene on chromosome 7q11.21, encoding Zinc finger protein 117 (Q03924). May be involved in transcriptional regulation.

This gene encodes a protein containing multiple C2H2-type zinc finger motifs. Readthrough transcription occurs between this gene and the upstream endogenous retrovirus group 3 member 1 (ERV3-1) locus, and may result in additional transcript variants encoding the zinc finger protein.

Source: NCBI Gene 51351 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_015852

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12897
Approved symbol	ZNF117
Name	zinc finger protein 117
Location	7q11.21
Locus type	gene with protein product
Status	Approved
Aliases	HPF9, H-plk
Ensembl gene	ENSG00000152926
Ensembl biotype	protein_coding
OMIM	194624
Entrez	51351

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 retained_intron

ENST00000282869, ENST00000487644, ENST00000714026, ENST00000714027, ENST00000956145

RefSeq mRNA: 2 — MANE Select: NM_015852 NM_001348050, NM_015852

Canonical transcript exons

ENST00000282869 — 4 exons

Exon	Start	End
ENSE00001534398	64989947	64991036
ENSE00001706697	64981984	64982116
ENSE00002525000	64981387	64981482
ENSE00004026238	64971772	64979536

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 98.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.7058 / max 302.5516, expressed in 1751 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
84203	20.7058	1751

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endometrium epithelium	UBERON:0004811	98.32	gold quality
frontal pole	UBERON:0002795	97.00	gold quality
adrenal tissue	UBERON:0018303	96.99	gold quality
paraflocculus	UBERON:0005351	96.91	gold quality
buccal mucosa cell	CL:0002336	95.47	gold quality
middle frontal gyrus	UBERON:0002702	93.45	gold quality
Brodmann (1909) area 10	UBERON:0013541	91.75	gold quality
right adrenal gland cortex	UBERON:0035827	91.71	gold quality
right adrenal gland	UBERON:0001233	91.05	gold quality
left adrenal gland	UBERON:0001234	91.00	gold quality
left adrenal gland cortex	UBERON:0035825	90.70	gold quality
adrenal cortex	UBERON:0001235	90.68	gold quality
adrenal gland	UBERON:0002369	90.26	gold quality
adipose tissue	UBERON:0001013	89.05	gold quality
ganglionic eminence	UBERON:0004023	88.94	gold quality
subcutaneous adipose tissue	UBERON:0002190	88.78	gold quality
adipose tissue of abdominal region	UBERON:0007808	88.40	gold quality
omental fat pad	UBERON:0010414	88.40	gold quality
peritoneum	UBERON:0002358	88.34	gold quality
connective tissue	UBERON:0002384	88.26	gold quality
cortical plate	UBERON:0005343	87.84	gold quality
placenta	UBERON:0001987	86.43	gold quality
parietal pleura	UBERON:0002400	85.19	gold quality
right uterine tube	UBERON:0001302	84.96	gold quality
visceral pleura	UBERON:0002401	84.82	gold quality
pleura	UBERON:0000977	84.53	gold quality
lower esophagus mucosa	UBERON:0035834	84.52	gold quality
gall bladder	UBERON:0002110	84.17	gold quality
right lung	UBERON:0002167	84.14	gold quality
tibia	UBERON:0000979	84.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	6.06

Regulation

Is transcription factor: no

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), ZNF221 (ENSG00000159905), ZNF235 (ENSG00000159917), ZNF714 (ENSG00000160352), ZNF577 (ENSG00000161551), ZNF12 (ENSG00000164631), ZNF3 (ENSG00000166526)

Protein

Protein identifiers

Zinc finger protein 117 — Q03924 (reviewed: Q03924)

Alternative names: Provirus-linked krueppel, Zinc finger protein HPF9

All UniProt accessions (1): Q03924

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 (2): NP_001334979, NP_056936* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF13465

UniProt features (19 total): zinc finger region 13, sequence conflict 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q03924-F1	75.57	0.30

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 142 (showing top): TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP, KOBAYASHI_EGFR_SIGNALING_24HR_UP, WANG_CLIM2_TARGETS_UP, MODULE_255, MODULE_317, MODULE_16, HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN, MODULE_205, TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN, GENTILE_UV_HIGH_DOSE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, MODULE_98, chr7q11, JAATINEN_HEMATOPOIETIC_STEM_CELL_UP

GO Biological Process (2): negative regulation of transcription by RNA polymerase II (GO:0000122), 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), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of transcription by RNA polymerase II	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	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
transcription cis-regulatory region binding	1
regulation of DNA-templated transcription	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF117	SS18	Q15532	766
ZNF117	SSX1	Q16384	760
ZNF117	SSX5	O60225	688
ZNF117	SSX3	Q99909	645
ZNF117	SSX4	O60224	639
ZNF117	OR2L8	Q8NGY9	506
ZNF117	MAGEB16	A2A368	479
ZNF117	MOB3C	Q70IA8	447
ZNF117	SPDYE2	Q495Y8	447
ZNF117	OR2T12	Q8NG77	446
ZNF117	CCDC144NL	Q6NUI1	419
ZNF117	OR10X1	Q8NGY0	418
ZNF117	OR51Q1	Q8NH59	417
ZNF117	OR10A5	Q9H207	398
ZNF117	OR5AR1	Q8NGP9	380

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ECE1	ZNF117	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): ZNF117 (Reconstituted Complex), ZNF117 (Cross-Linking-MS (XL-MS)), ZNF117 (Affinity Capture-RNA)

ESM2 similar proteins: A6NK75, A6NNF4, A6NP11, A8MTY0, B4DXR9, C9JN71, O75346, O75373, O75437, O95780, P0CJ79, P0DKX0, P0DPD5, P17017, P17019, P17035, P17038, P35789, Q03923, Q03924, Q03936, Q03938, Q08AN1, Q5MCW4, Q5R9F0, Q5SXM1, Q68DY1, Q6JLC9, Q6P5C7, Q6ZMV8, Q6ZN06, Q6ZN08, Q6ZNA1, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8IYN0, Q8N4W9

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

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

839 predictions. Top by Δscore:

Variant	Effect	Δscore
7:64981982:A:AT	donor_loss	1.0000
7:64981983:C:CA	donor_loss	1.0000
7:64982112:GGTCC:G	acceptor_gain	1.0000
7:64982113:GTCC:G	acceptor_gain	1.0000
7:64982114:TCC:T	acceptor_gain	1.0000
7:64982115:CC:C	acceptor_gain	1.0000
7:64982115:CCC:C	acceptor_gain	1.0000
7:64982116:CC:C	acceptor_gain	1.0000
7:64982117:C:CC	acceptor_gain	1.0000
7:64982117:CT:C	acceptor_loss	1.0000
7:65006537:TCAC:T	donor_loss	1.0000
7:65006539:ACCAT:A	donor_loss	1.0000
7:64981480:TACC:T	acceptor_loss	0.9900
7:64981483:C:CG	acceptor_loss	0.9900
7:64981491:T:TC	acceptor_gain	0.9900
7:64982029:G:A	donor_gain	0.9900
7:64982117:C:T	acceptor_gain	0.9900
7:64982127:C:CT	acceptor_gain	0.9900
7:65006537:T:A	donor_gain	0.9900
7:65006539:A:AC	donor_gain	0.9900
7:65006540:C:CC	donor_gain	0.9900
7:65006553:T:TA	donor_gain	0.9900
7:64981485:G:C	acceptor_loss	0.9800
7:64981983:CCT:C	donor_gain	0.9800
7:64981985:TTC:T	donor_gain	0.9800
7:64982128:A:T	acceptor_gain	0.9800
7:64993416:T:C	acceptor_gain	0.9800
7:65006539:AC:A	donor_gain	0.9800
7:65006540:CC:C	donor_gain	0.9800
7:64979532:CATAA:C	acceptor_gain	0.9700

AlphaMissense

3216 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:64978545:A:C	F342L	0.978
7:64978545:A:T	F342L	0.978
7:64978547:A:G	F342L	0.978
7:64978461:A:C	F370L	0.968
7:64978461:A:T	F370L	0.968
7:64978463:A:G	F370L	0.968
7:64978713:A:C	F286L	0.966
7:64978713:A:T	F286L	0.966
7:64978715:A:G	F286L	0.966
7:64978629:A:C	F314L	0.965
7:64978629:A:T	F314L	0.965
7:64978631:A:G	F314L	0.965
7:64978209:A:C	F454L	0.950
7:64978209:A:T	F454L	0.950
7:64978211:A:G	F454L	0.950
7:64978965:A:C	F202L	0.949
7:64978965:A:T	F202L	0.949
7:64978967:A:G	F202L	0.949
7:64979049:A:C	F174L	0.948
7:64979049:A:T	F174L	0.948
7:64979051:A:G	F174L	0.948
7:64978797:A:C	F258L	0.939
7:64978797:A:T	F258L	0.939
7:64978799:A:G	F258L	0.939
7:64978293:A:C	F426L	0.938
7:64978293:A:T	F426L	0.938
7:64978295:A:G	F426L	0.938
7:64978528:A:G	L348P	0.936
7:64978881:A:C	F230L	0.919
7:64978881:A:T	F230L	0.919

dbSNP variants (sampled 300 via entrez): RS1000023149 (7:64980008 G>T), RS1000315821 (7:64989997 G>A,C), RS1000366499 (7:64990290 C>A,T), RS1000699567 (7:64991348 T>A,C), RS1000802503 (7:64986268 T>C), RS1000833810 (7:64986562 T>C), RS1000936821 (7:64984882 C>A), RS1001001512 (7:64978756 G>C), RS1001074711 (7:64978960 T>C,G), RS1001149118 (7:64982448 T>C), RS1001181844 (7:64982782 T>A,C), RS1001424233 (7:64988834 C>A,T), RS1001461850 (7:64974470 GTACAT>G), RS1001510427 (7:64972207 C>T), RS1001673289 (7:64976152 C>G,T)

Disease associations

OMIM: gene MIM:194624 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, increases expression	2
Cyclosporine	decreases expression, increases methylation	2
GSK-J4	decreases expression	1
OTX015	increases expression	1
mivebresib	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
trichostatin A	increases expression	1
sodium arsenite	increases expression	1
avobenzone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
bisphenol S	increases expression	1
jinfukang	decreases expression	1
NSC 689534	affects binding, increases expression	1
(+)-JQ1 compound	increases expression	1
Rosiglitazone	decreases reaction, increases expression	1
Pioglitazone	increases expression, decreases reaction	1
Sunitinib	decreases expression	1
Troglitazone	decreases reaction, increases expression	1
Leflunomide	increases expression	1
Ethanol	affects cotreatment, increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	decreases expression	1
Copper	affects binding, increases expression	1
Coumestrol	decreases expression	1
Succimer	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1

Clinical trials (associated diseases)

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