ZNF414

Summary

ZNF414 (zinc finger protein 414, HGNC:20630) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 414 (Q96IQ9). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus.

Source: NCBI Gene 84330 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 89 total
• MANE Select transcript: NM_001146175

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20630
Approved symbol	ZNF414
Name	zinc finger protein 414
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC15716, Zfp414
Ensembl gene	ENSG00000133250
Ensembl biotype	protein_coding
OMIM	620980
Entrez	84330

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000255616, ENST00000393927, ENST00000593661, ENST00000594748, ENST00000595348, ENST00000596772, ENST00000599379, ENST00000600906, ENST00000602128

RefSeq mRNA: 2 — MANE Select: NM_001146175 NM_001146175, NM_032370

CCDS: CCDS12205, CCDS54211

Canonical transcript exons

ENST00000393927 — 8 exons

Exon	Start	End
ENSE00000910009	8511617	8511960
ENSE00000910012	8513029	8513341
ENSE00001516941	8510851	8511024
ENSE00001516942	8511486	8511536
ENSE00001658196	8509678	8510764
ENSE00003095870	8514044	8514167
ENSE00003508437	8512604	8512711
ENSE00003546179	8512387	8512492

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 91.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.1324 / max 178.4977, expressed in 1802 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178958	14.1256	1794
178956	1.4043	877
178957	0.4162	173
178954	0.1491	62
178955	0.0371	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	91.69	gold quality
lower esophagus mucosa	UBERON:0035834	91.53	gold quality
right lobe of thyroid gland	UBERON:0001119	90.78	gold quality
left lobe of thyroid gland	UBERON:0001120	90.70	gold quality
body of uterus	UBERON:0009853	90.66	gold quality
adenohypophysis	UBERON:0002196	90.30	gold quality
apex of heart	UBERON:0002098	90.26	gold quality
left ovary	UBERON:0002119	90.25	gold quality
ectocervix	UBERON:0012249	90.23	gold quality
endocervix	UBERON:0000458	90.13	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.85	gold quality
ventricular zone	UBERON:0003053	89.61	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.53	gold quality
right adrenal gland cortex	UBERON:0035827	89.48	gold quality
left uterine tube	UBERON:0001303	89.26	gold quality
right uterine tube	UBERON:0001302	89.12	gold quality
left adrenal gland	UBERON:0001234	89.06	gold quality
ganglionic eminence	UBERON:0004023	89.05	gold quality
embryo	UBERON:0000922	89.04	gold quality
right adrenal gland	UBERON:0001233	89.04	gold quality
right ovary	UBERON:0002118	88.98	gold quality
left adrenal gland cortex	UBERON:0035825	88.95	gold quality
mucosa of transverse colon	UBERON:0004991	88.92	gold quality
cerebellar hemisphere	UBERON:0002245	88.78	gold quality
cerebellar cortex	UBERON:0002129	88.68	gold quality
mucosa of stomach	UBERON:0001199	88.66	gold quality
metanephros cortex	UBERON:0010533	88.66	gold quality
skin of abdomen	UBERON:0001416	88.55	gold quality
right frontal lobe	UBERON:0002810	88.53	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-124858	no	3.11
E-ANND-3	no	2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

4 targeting ZNF414, 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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-4477B	99.23	70.49	1733

Literature-anchored findings (GeneRIF, showing 1)

• KPNA7 binding and nuclear transfer was validated for two proteins, MVP and ZNF414. MVP and ZNF414 have a key role in the regulation of pancreatic cancer cell growth. (PMID:27664836)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	znf414	ENSDARG00000079229
mus_musculus	Zfp414	ENSMUSG00000073423
rattus_norvegicus	Zfp414	ENSRNOG00000008378

Protein

Protein identifiers

Zinc finger protein 414 — Q96IQ9 (reviewed: Q96IQ9)

All UniProt accessions (5): Q96IQ9, M0R0Q5, M0R1G8, M0R2Q9, M0R398

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?
Q96IQ9-1	1	yes
Q96IQ9-2	2

RefSeq proteins (2): NP_001139647, NP_115746 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR031799	Znf-C2H2_ribbon	Domain
IPR039882	ZN414	Family

Pfam: PF15909

UniProt features (15 total): compositionally biased region 5, zinc finger region 3, sequence variant 2, region of interest 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96IQ9-F1	60.86	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 76 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, SP1_Q2_01, EGR1_01, chr19p13, WHITFIELD_CELL_CYCLE_G1_S, EGR_Q6, MYC_UP.V1_DN, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ALKBH3_TARGET_GENES, ARID5B_TARGET_GENES, BANP_TARGET_GENES, DYRK1A_TARGET_GENES, FOXN3_TARGET_GENES, GLI1_TARGET_GENES

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), protein binding (GO:0005515), 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
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
regulation of DNA-templated transcription	1
transcription regulator activity	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

570 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF414	ACTMAP	Q5BKX5	446
ZNF414	CCDC97	Q96F63	435
ZNF414	FAM124A	Q86V42	433
ZNF414	TSPAN13	O95857	424
ZNF414	R3HCC1	Q9Y3T6	421
ZNF414	ZNF32	P17041	404
ZNF414	HDHD5	Q9BXW7	397
ZNF414	SEC22A	Q96IW7	388
ZNF414	MED31	Q9Y3C7	382
ZNF414	ZNF823	P16415	370
ZNF414	TRABD	Q9H4I3	370
ZNF414	BEND6	Q5SZJ8	367
ZNF414	GOLT1B	Q9Y3E0	357
ZNF414	FBXW2	Q9UKT8	348
ZNF414	RNF14	Q9UBS8	343

IntAct

180 interactions, top by confidence:

A	B	Type	Score
GOLGA2	ZNF414	psi-mi:“MI:0915”(physical association)	0.780
ZNF414	GOLGA2	psi-mi:“MI:0915”(physical association)	0.780
ZNF414	AHCYL1	psi-mi:“MI:0914”(association)	0.640
ZNF414	TRIM42	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	KRTAP9-3	psi-mi:“MI:0915”(physical association)	0.560
NOTCH2NLC	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
KRTAP6-3	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
GOLGA6L9	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
ADAMTSL4	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
TRIM27	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
KRT34	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
KRTAP1-3	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	TRIM10	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	RBCK1	psi-mi:“MI:0915”(physical association)	0.560
MTUS2	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	HOMER3	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	PICK1	psi-mi:“MI:0915”(physical association)	0.560
MKRN3	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
PDE4DIP	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	CARD10	psi-mi:“MI:0915”(physical association)	0.560
TEX11	ZNF414	psi-mi:“MI:0915”(physical association)	0.560
ZNF414	MDFI	psi-mi:“MI:0915”(physical association)	0.560
KANK2	ZNF414	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (153): ZNF414 (Two-hybrid), NPRL3 (Affinity Capture-MS), KDM4B (Affinity Capture-MS), EDRF1 (Affinity Capture-MS), PPP1R1A (Affinity Capture-MS), DEPDC5 (Affinity Capture-MS), NPRL2 (Affinity Capture-MS), HSD17B8 (Affinity Capture-MS), ANGEL1 (Affinity Capture-MS), ZNF414 (Two-hybrid), KDM4B (Affinity Capture-MS), KDM4A (Affinity Capture-MS), ZRANB1 (Affinity Capture-MS), ANKRD50 (Affinity Capture-MS), NOC4L (Affinity Capture-MS)

ESM2 similar proteins: A0A8I5KY20, A4IHR5, A7UKY7, A8IHN8, D3YYI7, G3V9M2, O43559, P39881, P49796, Q13387, Q14DQ1, Q2TAM9, Q32KV8, Q3UPL5, Q4VA45, Q5VUJ9, Q5VV17, Q5XKK7, Q62392, Q673H1, Q6NV74, Q6PJ61, Q6QHK4, Q6UXB0, Q7Z6J2, Q80TE3, Q86SH2, Q8BWU3, Q8CE64, Q8IWP9, Q8N554, Q8NFT6, Q8R4T5, Q8TC41, Q8VCC6, Q8WV24, Q96HA4, Q96IQ9, Q96SQ7, Q96T92

Diamond homologs: Q32KV8, Q5PPH4, Q96IQ9, Q9DCK4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 56 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	17	25.6×	2e-18

GO biological processes:

GO term	Partners	Fold	FDR
keratinization	5	26.6×	3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1125 predictions. Top by Δscore:

Variant	Effect	Δscore
19:8511021:TGCC:T	acceptor_gain	1.0000
19:8511021:TGCCC:T	acceptor_loss	1.0000
19:8511022:GCCCT:G	acceptor_loss	1.0000
19:8511023:CC:C	acceptor_gain	1.0000
19:8511024:CC:C	acceptor_gain	1.0000
19:8511024:CCTG:C	acceptor_loss	1.0000
19:8511025:C:CC	acceptor_gain	1.0000
19:8511025:CTGC:C	acceptor_loss	1.0000
19:8511026:T:C	acceptor_loss	1.0000
19:8511481:CGCA:C	donor_loss	1.0000
19:8511482:GCACC:G	donor_loss	1.0000
19:8511483:CA:C	donor_loss	1.0000
19:8511538:T:A	acceptor_loss	1.0000
19:8511541:G:T	acceptor_gain	1.0000
19:8511542:G:GC	acceptor_gain	1.0000
19:8511612:CTCA:C	donor_loss	1.0000
19:8511613:TCA:T	donor_loss	1.0000
19:8511614:CA:C	donor_loss	1.0000
19:8511615:AC:A	donor_gain	1.0000
19:8511616:CC:C	donor_gain	1.0000
19:8512385:A:AC	donor_gain	1.0000
19:8512386:C:CC	donor_gain	1.0000
19:8512502:A:C	acceptor_gain	1.0000
19:8512600:CTAC:C	donor_loss	1.0000
19:8512601:TA:T	donor_loss	1.0000
19:8512602:ACC:A	donor_loss	1.0000
19:8514043:CCAT:C	donor_gain	1.0000
19:8511020:GTGCC:G	acceptor_gain	0.9900
19:8511022:GCC:G	acceptor_gain	0.9900
19:8511023:CCC:C	acceptor_gain	0.9900

AlphaMissense

2481 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:8511937:A:G	F185S	1.000
19:8511909:G:C	H194Q	0.999
19:8511909:G:T	H194Q	0.999
19:8511911:G:C	H194D	0.999
19:8511911:G:T	H194N	0.999
19:8511919:A:G	L191P	0.999
19:8511936:G:C	F185L	0.999
19:8511936:G:T	F185L	0.999
19:8511938:A:G	F185L	0.999
19:8511948:G:C	C181W	0.999
19:8511950:A:G	C181R	0.999
19:8511959:A:G	C178R	0.999
19:8512389:G:C	F176L	0.999
19:8512389:G:T	F176L	0.999
19:8512390:A:G	F176S	0.999
19:8512391:A:G	F176L	0.999
19:8512432:A:G	L162P	0.999
19:8512478:A:G	C147R	0.999
19:8511907:A:G	L195P	0.998
19:8511910:T:C	H194R	0.998
19:8511912:C:A	K193N	0.998
19:8511912:C:G	K193N	0.998
19:8511916:A:G	F192S	0.998
19:8511949:C:T	C181Y	0.998
19:8511958:C:G	C178S	0.998
19:8511959:A:T	C178S	0.998
19:8512390:A:C	F176C	0.998
19:8512404:T:A	K171N	0.998
19:8512404:T:G	K171N	0.998
19:8512461:G:C	C152W	0.998

dbSNP variants (sampled 300 via entrez): RS1000887123 (19:8511029 G>A,T), RS1001164823 (19:8511997 C>T), RS1001887416 (19:8512260 C>A,T), RS1001918505 (19:8511983 G>A,C,T), RS1002900278 (19:8513268 T>A), RS1002923276 (19:8513120 G>A), RS1003729261 (19:8515659 C>T), RS1003886242 (19:8513874 G>A,T), RS1003938079 (19:8514175 T>C,G), RS1004095254 (19:8509215 T>C), RS1004709656 (19:8509975 G>A), RS1004939008 (19:8515487 C>G), RS1005062884 (19:8510535 G>A,C,T), RS1005503801 (19:8510172 C>A,T), RS1005828824 (19:8512311 G>A,C)

Disease associations

OMIM: gene MIM:620980 | 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

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, increases expression	2
Arsenic	increases methylation, affects methylation	2
bisphenol F	affects cotreatment, increases expression	1
kojic acid	decreases expression	1
sodium arsenite	increases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
cylindrospermopsin	increases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Acetaminophen	decreases expression	1
Arbutin	decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	decreases expression	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_XW43	HEK293 eGFP-ZNF414	Transformed cell line	Female

Clinical trials (associated diseases)

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