NFILZ

Summary

NFILZ (NFIL3 like basic leucine zipper, HGNC:52681) is a protein-coding gene on chromosome 19p13.2, encoding NFIL3 like protein (A0A5F9ZHS7).

Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in circadian rhythm and regulation of DNA-templated transcription. Predicted to be active in nucleus.

Source: NCBI Gene 105372267 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GTEx eGene: eQTL in 1 tissue, sQTL in 0 (q < 0.05)
• MANE Select transcript: NM_001378600

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:52681
Approved symbol	NFILZ
Name	NFIL3 like basic leucine zipper
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000268480
Ensembl biotype	protein_coding
Entrez	105372267

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000691075

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 2: 1

ENST00000691075, ENST00000570582, ENST00000593792, ENST00000663339, ENST00000671902, ENST00000673603

RefSeq mRNA: 3 — MANE Select: NM_001378600 NM_001378599, NM_001378600, NM_001378601

CCDS: CCDS92505

Canonical transcript exons

ENST00000691075 — 6 exons

Exon	Start	End
ENSE00002640251	8676751	8681151
ENSE00003147153	8635650	8635746
ENSE00003172134	8632476	8632625
ENSE00003888709	8674551	8674600
ENSE00003891378	8676359	8676456
ENSE00003933609	8630633	8630744

Expression profiles

Bgee: expression breadth broad, 48 present calls, max score 91.24.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0439 / max 15.7880, expressed in 20 samples.

Highest expression (Bgee): thymus, male germ line stem cell (sensu Vertebrata) in testis, cerebellar vermis, quadriceps femoris, testis.

Genetic regulation across tissues (GTEx eQTL / sQTL)

NFILZ is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 1 tissue and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

1 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Whole Blood	eqtl	5.6e-05	-0.37	19:8675560:G:A

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
173688	0.0301	17
173687	0.0137	3

Top tissues by expression

93 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
thymus	UBERON:0002370	91.24	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.23	gold quality
cerebellar vermis	UBERON:0004720	81.72	gold quality
quadriceps femoris	UBERON:0001377	79.70	gold quality
left testis	UBERON:0004533	70.05	gold quality
testis	UBERON:0000473	69.88	gold quality
right testis	UBERON:0004534	69.22	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.08	gold quality
granulocyte	CL:0000094	49.49	silver quality
endometrium	UBERON:0001295	46.83	gold quality
placenta	UBERON:0001987	43.82	gold quality
stromal cell of endometrium	CL:0002255	43.26	silver quality
mucosa of transverse colon	UBERON:0004991	42.14	silver quality
blood	UBERON:0000178	42.10	gold quality
vermiform appendix	UBERON:0001154	39.81	silver quality
lymph node	UBERON:0000029	39.44	gold quality
bone marrow	UBERON:0002371	38.91	silver quality
bone marrow cell	CL:0002092	38.51	gold quality
calcaneal tendon	UBERON:0003701	38.39	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
leukocyte	CL:0000738	36.20	silver quality
hindlimb stylopod muscle	UBERON:0004252	35.92	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
liver	UBERON:0002107	34.93	silver quality
gall bladder	UBERON:0002110	34.38	silver quality
monocyte	CL:0000576	34.33	gold quality
skeletal muscle tissue	UBERON:0001134	34.04	silver quality
rectum	UBERON:0001052	32.79	silver quality
muscle tissue	UBERON:0002385	32.74	silver quality
sural nerve	UBERON:0015488	30.93	gold quality
prefrontal cortex	UBERON:0000451	30.05	silver quality
right uterine tube	UBERON:0001302	29.77	gold quality
islet of Langerhans	UBERON:0000006	29.73	gold quality
corpus callosum	UBERON:0002336	28.94	gold quality
myometrium	UBERON:0001296	28.90	gold quality
thoracic mammary gland	UBERON:0005200	28.73	silver quality
right lobe of liver	UBERON:0001114	28.67	gold quality
urinary bladder	UBERON:0001255	28.63	gold quality
duodenum	UBERON:0002114	28.14	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	28.14	silver quality
muscle of leg	UBERON:0001383	28.12	gold quality
pancreas	UBERON:0001264	27.94	silver quality
smooth muscle tissue	UBERON:0001135	27.82	gold quality
multicellular organism	UBERON:0000468	27.69	gold quality
spinal cord	UBERON:0002240	26.85	silver quality
C1 segment of cervical spinal cord	UBERON:0006469	26.62	silver quality
gastrocnemius	UBERON:0001388	26.59	gold quality
lung	UBERON:0002048	26.42	gold quality
adult mammalian kidney	UBERON:0000082	26.30	silver quality
frontal cortex	UBERON:0001870	25.84	silver quality
body of pancreas	UBERON:0001150	25.81	silver quality
substantia nigra	UBERON:0002038	25.39	gold quality
right lung	UBERON:0002167	24.75	gold quality
primary visual cortex	UBERON:0002436	24.61	gold quality
putamen	UBERON:0001874	24.39	gold quality
cerebral cortex	UBERON:0000956	24.17	silver quality
superior frontal gyrus	UBERON:0002661	24.08	gold quality
omental fat pad	UBERON:0010414	24.07	silver quality
tibial nerve	UBERON:0001323	24.06	gold quality
stomach	UBERON:0000945	23.97	gold quality
heart	UBERON:0000948	23.84	silver quality
upper lobe of left lung	UBERON:0008952	23.60	gold quality
skin of abdomen	UBERON:0001416	23.56	gold quality
brain	UBERON:0000955	23.41	gold quality
hypothalamus	UBERON:0001898	23.31	gold quality
Ammon’s horn	UBERON:0001954	23.26	silver quality
small intestine	UBERON:0002108	23.20	gold quality
fallopian tube	UBERON:0003889	22.95	gold quality
anterior cingulate cortex	UBERON:0009835	22.85	gold quality
Brodmann (1909) area 9	UBERON:0013540	22.76	silver quality
left coronary artery	UBERON:0001626	22.71	gold quality
left lobe of thyroid gland	UBERON:0001120	22.70	gold quality
body of stomach	UBERON:0001161	22.56	gold quality
adrenal tissue	UBERON:0018303	22.34	gold quality
endocervix	UBERON:0000458	22.23	silver quality
lower esophagus mucosa	UBERON:0035834	22.15	gold quality
vagina	UBERON:0000996	22.12	gold quality
cerebellum	UBERON:0002037	22.09	gold quality
cerebellar cortex	UBERON:0002129	21.93	gold quality
small intestine Peyer’s patch	UBERON:0003454	21.68	gold quality
cerebellar hemisphere	UBERON:0002245	21.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	21.59	gold quality
fundus of stomach	UBERON:0001160	21.24	gold quality
apex of heart	UBERON:0002098	20.28	gold quality
ectocervix	UBERON:0012249	19.78	gold quality
right frontal lobe	UBERON:0002810	19.77	gold quality
right coronary artery	UBERON:0001625	19.38	gold quality
adenohypophysis	UBERON:0002196	18.79	gold quality
right ovary	UBERON:0002118	18.70	gold quality
mucosa of stomach	UBERON:0001199	18.29	gold quality
left uterine tube	UBERON:0001303	17.33	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	25.46
E-ANND-3	no	1.48

HPA expression

RNA tissue specificity: Tissue enhanced

39 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Postcentral gyrus	tissue	9.3
Choroid plexus	tissue	8.3
Hippocampus	tissue	7.9
Nucleus accumbens	tissue	7.7
Locus coeruleus	tissue	7.7
Testis	tissue	1.5
Bone marrow	tissue	0.7
Retina	tissue	0.5
Skin 1	tissue	0.4
Skeletal muscle	tissue	0.4
Spleen	tissue	0.3
Lymph node	tissue	0.2
Stomach 1	tissue	0.2
Endometrium 1	tissue	0.2
Lung	tissue	0.2
Liver	tissue	0.2
Kidney	tissue	0.2
Thymus	tissue	0.2
Tonsil	tissue	0.2
Appendix	tissue	0.2
Breast	tissue	0.1
Heart muscle	tissue	0.1
Seminal vesicle	tissue	0.1
Adipose tissue	tissue	0.1
Esophagus	tissue	0.1
Salivary gland	tissue	0.1
Rectum	tissue	0.1
Smooth muscle	tissue	0.1
Colon	tissue	0.1
Urinary bladder	tissue	0.1
Epididymis	tissue	0.1
Placenta	tissue	0.1
Thyroid gland	tissue	0.1
Small intestine	tissue	0.1
Gallbladder	tissue	0.1
Duodenum	tissue	0.1
Spinal cord	tissue	0.1
Prostate	tissue	0.1
Fallopian tube	tissue	0.1

Brain sub-regions (HPA Brain Atlas): detected in 183; highest nTPM — Area striata (white matter) (11.4), Parietal operculum (11.0), Vermis (11.0), Gigantocellular reticular nuclei, pars (10.8), Orbitofrontal gyrus, anterior (10.8).

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-172o19.2	ENSDARG00000071398
danio_rerio	nfil3-4	ENSDARG00000092346
mus_musculus	Nfilz	ENSMUSG00000117495
rattus_norvegicus	Nfilz	ENSRNOG00000063608
drosophila_melanogaster	vri	FBGN0016076
caenorhabditis_elegans		WBGENE00000220

Paralogs (1): NFIL3 (ENSG00000165030)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Xenopus tropicalis	Q5FW38	92.6%	Diamond
Xenopus laevis	Q66J36	92.6%	Diamond
Bos taurus	Q32PF6	92.0%	Diamond
Gallus gallus	Q92172	87.9%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
ZNF558	protein-coding	148156
ACTL9	protein-coding	284382
OR2Z1	protein-coding	284383
MBD3L1	protein-coding	85509
MUC16	protein-coding	94025
MYO1F	protein-coding	4542
ADAMTS10	protein-coding	81794
PRAM1	protein-coding	84106
ZNF414	protein-coding	84330

Protein

Protein identifiers

NFIL3 like protein — A0A5F9ZHS7 (reviewed: A0A5F9ZHS7)

Alternative names: NFIL3 like basic leucine zipper

All UniProt accessions (1): A0A5F9ZHS7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the bZIP family. NFIL3 subfamily.

RefSeq proteins (3): NP_001365528, NP_001365529, NP_001365530 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004827	bZIP	Domain
IPR046347	bZIP_sf	Homologous_superfamily
IPR047106	NFIL3-like_bZIP	Domain
IPR047229	NFIL3-like	Family

Pfam: PF07716

UniProt features (5 total): region of interest 3, chain 1, domain 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A5F9ZHS7-F1	59.84	0.20

Human Protein Atlas

Protein class: Predicted intracellular proteins, UniProt - Inferred from homology

Protein evidence: Evidence at protein level

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 8 (showing top): GOBP_CIRCADIAN_RHYTHM, chr19p13, GOBP_RHYTHMIC_PROCESS, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, SMN1_SMN2_TARGET_GENES, DESCARTES_MAIN_FETAL_ELF3_AGBL2_POSITIVE_CELLS, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, ZNF248_TARGET_GENES

GO Biological Process (3): DNA-templated transcription (GO:0006351), regulation of DNA-templated transcription (GO:0006355), circadian rhythm (GO:0007623)

GO Molecular Function (2): DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700)

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

GO top-level categories

11 GO namespaces:

Category	Terms
gene expression	1
RNA biosynthetic process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
rhythmic process	1
nucleic acid binding	1
transcription cis-regulatory region binding	1
regulation of DNA-templated transcription	1
transcription regulator activity	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

showing 16 of 534 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NFILZ	HSFX4	A0A1B0GTS1	719
NFILZ	ZNF738	Q8NE65	606
NFILZ	ZBED5	Q49AG3	570
NFILZ	FOXO3B	A0A2Z4LIS9	510
NFILZ	MIER3	Q7Z3K6	492
NFILZ	TCF25	Q9BQ70	428
NFILZ	TCF19	Q9Y242	386
NFILZ	POMC	P01189	363
NFILZ	F8	P00451	360
NFILZ	LEP	P41159	357
NFILZ	ANXA3	P12429	322
NFILZ	ANXA5	P08758	322
NFILZ	ANXA11	P50995	322
NFILZ	NANS	Q9NR45	315
NFILZ	SDR42E1	Q8WUS8	313
NFILZ	TIMELESS	Q9UNS1	313

Disease & clinical

Genetic variants

ClinVar

No ClinVar records for this gene.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 27 predictions of 452):

Position(s)	Effect	Δscore	Sites
19:8674549–8674550	acceptor_loss	1.0000	6
19:8674601–8674602	donor_loss	1.0000	3
19:8674601	donor_loss	0.9900
19:8638619	donor_gain	0.9800
19:8638669	donor_gain	0.9800
19:8671849	donor_gain	0.9800
19:8674601	donor_loss	0.9800
19:8676749–8676750	acceptor_loss	0.9800	6
19:8630762	donor_gain	0.9700
19:8677022–8677023	donor_loss	0.9700	6

HPA cancer prognostics

RNA cancer specificity: Not detected

Disease associations

OMIM: gene `` | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.