ZNF619

Summary

ZNF619 (zinc finger protein 619, HGNC:26910) is a protein-coding gene on chromosome 3p22.1, encoding Zinc finger protein 619 (Q8N2I2). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 285267 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 106 total
• MANE Select transcript: NM_001145093

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26910
Approved symbol	ZNF619
Name	zinc finger protein 619
Location	3p22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90764
Ensembl gene	ENSG00000177873
Ensembl biotype	protein_coding
Entrez	285267

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000314686, ENST00000429348, ENST00000432264, ENST00000447116, ENST00000456778, ENST00000462961, ENST00000494154, ENST00000520737, ENST00000521353, ENST00000522736, ENST00000864078

RefSeq mRNA: 6 — MANE Select: NM_001145093 NM_001145082, NM_001145083, NM_001145093, NM_001145094, NM_001363277, NM_173656

CCDS: CCDS46801, CCDS46802, CCDS46803

Canonical transcript exons

ENST00000432264 — 5 exons

Exon	Start	End
ENSE00003584767	40481863	40482016
ENSE00003657884	40477918	40478003
ENSE00003663019	40482588	40482704
ENSE00003889889	40486806	40491053
ENSE00003893842	40477122	40477357

Expression profiles

Bgee: expression breadth ubiquitous, 159 present calls, max score 75.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5788 / max 82.5033, expressed in 1655 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36183	5.5788	1655

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	75.13	gold quality
colonic epithelium	UBERON:0000397	74.99	gold quality
islet of Langerhans	UBERON:0000006	74.36	gold quality
ventricular zone	UBERON:0003053	74.21	gold quality
bone marrow cell	CL:0002092	73.92	silver quality
smooth muscle tissue	UBERON:0001135	72.03	gold quality
leukocyte	CL:0000738	71.74	gold quality
ganglionic eminence	UBERON:0004023	71.60	gold quality
monocyte	CL:0000576	71.50	gold quality
stromal cell of endometrium	CL:0002255	71.19	gold quality
hindlimb stylopod muscle	UBERON:0004252	71.19	gold quality
rectum	UBERON:0001052	70.66	gold quality
muscle of leg	UBERON:0001383	70.44	gold quality
gastrocnemius	UBERON:0001388	69.94	gold quality
granulocyte	CL:0000094	69.72	gold quality
pancreas	UBERON:0001264	69.67	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	69.52	gold quality
body of pancreas	UBERON:0001150	68.30	gold quality
apex of heart	UBERON:0002098	68.08	gold quality
right adrenal gland	UBERON:0001233	68.05	gold quality
vermiform appendix	UBERON:0001154	67.69	gold quality
left adrenal gland	UBERON:0001234	67.67	gold quality
descending thoracic aorta	UBERON:0002345	67.67	gold quality
right adrenal gland cortex	UBERON:0035827	67.67	gold quality
sural nerve	UBERON:0015488	67.57	gold quality
right coronary artery	UBERON:0001625	67.50	gold quality
right lobe of liver	UBERON:0001114	67.38	gold quality
mucosa of transverse colon	UBERON:0004991	67.14	gold quality
left coronary artery	UBERON:0001626	67.00	gold quality
heart left ventricle	UBERON:0002084	66.97	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.23

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZFP37 (ENSG00000136866), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 619 — Q8N2I2 (reviewed: Q8N2I2)

All UniProt accessions (3): Q8N2I2, E5RJF3, Q17RW3

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 (4)

UniProt ID	Names	Canonical?
Q8N2I2-1	1	yes
Q8N2I2-2	2
Q8N2I2-3	3
Q8N2I2-4	4

RefSeq proteins (6): NP_001138554, NP_001138555, NP_001138565, NP_001138566, NP_001350206, NP_775927 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096

UniProt features (14 total): zinc finger region 10, splice variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N2I2-F1	61.64	0.28

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 43 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, KOYAMA_SEMA3B_TARGETS_UP, chr3p22, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, NFE2L1_TARGET_GENES, NFKBIA_TARGET_GENES, SNIP1_TARGET_GENES, MIR3662, MIR3680_3P, MIR1185_1_3P_MIR1185_2_3P, LET_7F_2_3P, MIR7106_5P, MIR4731_5P

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 transcription regulatory region sequence-specific DNA binding (GO:0000977), 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), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (1): 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
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
transcription cis-regulatory region binding	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

378 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF619	CNKSR3	Q6P9H4	474
ZNF619	PBX4	Q9BYU1	420
ZNF619	PDZK1IP1	Q13113	391
ZNF619	CRADD	P78560	348
ZNF619	MIEF1	Q9NQG6	321
ZNF619	ORMDL3	Q8N138	305
ZNF619	SAA1	P02735	240
ZNF619	SAA1	P02735	226
ZNF619	TAF6L	Q9Y6J9	221
ZNF619	TFAP4	Q01664	213
ZNF619	L3MBTL2	Q969R5	208
ZNF619	RBM14	Q96PK6	207
ZNF619	CXXC1	Q9P0U4	204
ZNF619	RNF141	Q8WVD5	201
ZNF619	USF2	Q15853	199

IntAct

7 interactions, top by confidence:

A	B	Type	Score
ZNF619	ECE1	psi-mi:“MI:0915”(physical association)	0.370
ECE1	ZNF619	psi-mi:“MI:0915”(physical association)	0.370
APP	ZNF619	psi-mi:“MI:0915”(physical association)	0.000
TULP3	ZNF619	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): ZNF619 (Synthetic Growth Defect), ZNF619 (Two-hybrid), ZNF619 (Two-hybrid)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2A761, A7MBI1, B2RUI1, D3ZVT0, P0CG31, P10072, P21506, P51814, P52738, Q02525, Q08ER8, Q09FC8, Q14590, Q16600, Q2M3X9, Q2VY69, Q3KQV3, Q3SY52, Q4V8A8, Q571J5, Q5CZA5, Q5R8G9, Q5RB33, Q5VIY5, Q61967, Q6NX49, Q6PG37, Q6ZMS4, Q6ZMW2, Q6ZNG0, Q80YP6, Q8IYX0, Q8IZ26, Q8N2I2, Q8N782, Q8N9Z0, Q8NEK5, Q8NHY6

Diamond homologs: A0JPL0, A3KN36, A6NFI3, A6NM28, A6QLU5, A6QPT6, A8MT65, B2RXC5, B4DU55, C9JBD0, O60765, O75467, P10072, P17014, P17023, P17097, P17098, P21506, P52736, P52738, P59923, Q02975, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14929, Q16587, Q29RZ4, Q32M78, Q3KNS6, Q3V080, Q49AA0, Q4R6C2, Q4R8H9, Q4V8E9, Q571J5, Q5CZA5, Q5FWF6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

106 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

974 predictions. Top by Δscore:

Variant	Effect	Δscore
3:40477180:GGT:G	donor_gain	0.9900
3:40477331:G:GT	donor_gain	0.9900
3:40482015:GT:G	donor_gain	0.9900
3:40482017:G:GG	donor_gain	0.9900
3:40482586:A:AG	acceptor_gain	0.9900
3:40482587:G:GG	acceptor_gain	0.9900
3:40482587:GC:G	acceptor_gain	0.9900
3:40482587:GCA:G	acceptor_gain	0.9900
3:40482587:GCAGC:G	acceptor_gain	0.9900
3:40477222:G:GT	donor_gain	0.9800
3:40477368:G:T	donor_gain	0.9800
3:40478829:T:TA	acceptor_gain	0.9800
3:40481977:G:T	donor_gain	0.9800
3:40486804:AGGT:A	acceptor_gain	0.9800
3:40486805:GGTG:G	acceptor_gain	0.9800
3:40477182:T:G	donor_gain	0.9700
3:40477353:T:TA	donor_gain	0.9700
3:40477386:C:G	donor_gain	0.9700
3:40477459:GACAT:G	donor_gain	0.9700
3:40477144:C:G	donor_gain	0.9600
3:40478894:G:GT	donor_gain	0.9600
3:40482215:T:TA	acceptor_gain	0.9600
3:40486800:TGCTA:T	acceptor_loss	0.9600
3:40486801:GCTA:G	acceptor_loss	0.9600
3:40486802:CTAG:C	acceptor_loss	0.9600
3:40486803:TAG:T	acceptor_loss	0.9600
3:40477354:CGC:C	donor_gain	0.9500
3:40477355:GCG:G	donor_gain	0.9500
3:40477368:G:GT	donor_gain	0.9500
3:40477372:G:GT	donor_gain	0.9500

AlphaMissense

3817 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:40487315:T:C	F253L	0.997
3:40487317:C:A	F253L	0.997
3:40487317:C:G	F253L	0.997
3:40487231:T:C	F225L	0.995
3:40487233:C:A	F225L	0.995
3:40487233:C:G	F225L	0.995
3:40487483:T:C	F309L	0.995
3:40487485:C:A	F309L	0.995
3:40487485:C:G	F309L	0.995
3:40487819:T:C	F421L	0.994
3:40487821:C:A	F421L	0.994
3:40487821:C:G	F421L	0.994
3:40487903:T:C	F449L	0.994
3:40487905:C:A	F449L	0.994
3:40487905:C:G	F449L	0.994
3:40487399:T:C	F281L	0.992
3:40487401:C:A	F281L	0.992
3:40487401:C:G	F281L	0.992
3:40487256:G:C	R233P	0.991
3:40487853:G:C	R432P	0.991
3:40487430:A:C	Q291P	0.990
3:40487260:T:A	H234Q	0.989
3:40487260:T:G	H234Q	0.989
3:40487262:A:C	Q235P	0.989
3:40487334:T:C	L259P	0.989
3:40487651:T:C	F365L	0.989
3:40487653:C:A	F365L	0.989
3:40487653:C:G	F365L	0.989
3:40487766:A:C	Q403P	0.989
3:40487850:A:C	Q431P	0.989

dbSNP variants (sampled 300 via entrez): RS1000310138 (3:40484648 C>G,T), RS1000373580 (3:40491520 T>A), RS1000425734 (3:40491248 G>C), RS1000819198 (3:40477137 C>T), RS1000856028 (3:40483390 A>G), RS1000991368 (3:40483746 A>C), RS1000997174 (3:40486135 G>A), RS1001006700 (3:40480375 C>T), RS1001086352 (3:40476846 A>G), RS1001221427 (3:40483747 A>C,G), RS1001377246 (3:40490058 T>C), RS1001429651 (3:40489755 G>A), RS1001494890 (3:40480159 A>C), RS1001545211 (3:40486599 G>T), RS1001714969 (3:40483511 G>C)

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
GCST005232_29	Neuroticism	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007660	neuroticism measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Ozone	affects expression, increases abundance	1
Testosterone	decreases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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