ZNF600

Summary

ZNF600 (zinc finger protein 600, HGNC:30951) is a protein-coding gene on chromosome 19q13.42, encoding Zinc finger protein 600 (Q6ZNG1). May be involved in transcriptional regulation.

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 162966 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 157 total
• MANE Select transcript: NM_001321866

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30951
Approved symbol	ZNF600
Name	zinc finger protein 600
Location	19q13.42
Locus type	gene with protein product
Status	Approved
Aliases	KR-ZNF1, DKFZp686F06123
Ensembl gene	ENSG00000189190
Ensembl biotype	protein_coding
Entrez	162966

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 20 protein_coding, 2 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000338230, ENST00000598369, ENST00000599893, ENST00000647907, ENST00000648893, ENST00000648973, ENST00000685388, ENST00000688329, ENST00000692063, ENST00000880463, ENST00000880464, ENST00000880465, ENST00000880466, ENST00000880467, ENST00000880468, ENST00000880469, ENST00000880470, ENST00000929806, ENST00000929807, ENST00000929808, ENST00000941328, ENST00000941329, ENST00000941330, ENST00000941331

RefSeq mRNA: 3 — MANE Select: NM_001321866 NM_001321866, NM_001321867, NM_198457

CCDS: CCDS12856, CCDS92675

Canonical transcript exons

ENST00000692063 — 6 exons

Exon	Start	End
ENSE00002999669	52781317	52781464
ENSE00003032870	52780581	52781055
ENSE00003050514	52786595	52786791
ENSE00003839668	52774575	52774701
ENSE00003841018	52778826	52778907
ENSE00003937606	52764184	52767772

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 93.83.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1463 / max 128.8451, expressed in 1454 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182533	4.9665	1436
182534	0.1799	64

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	93.83	gold quality
epithelial cell of pancreas	CL:0000083	93.21	gold quality
granulocyte	CL:0000094	92.46	gold quality
ileal mucosa	UBERON:0000331	89.65	gold quality
oocyte	CL:0000023	89.22	gold quality
secondary oocyte	CL:0000655	89.12	gold quality
esophagus squamous epithelium	UBERON:0006920	87.39	gold quality
cerebellar cortex	UBERON:0002129	87.29	gold quality
cerebellar hemisphere	UBERON:0002245	87.29	gold quality
visceral pleura	UBERON:0002401	86.96	gold quality
jejunal mucosa	UBERON:0000399	86.87	gold quality
parietal pleura	UBERON:0002400	86.74	gold quality
cerebellum	UBERON:0002037	86.70	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.59	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.53	gold quality
amniotic fluid	UBERON:0000173	86.29	gold quality
colonic mucosa	UBERON:0000317	86.08	gold quality
epithelium of nasopharynx	UBERON:0001951	86.08	gold quality
lower esophagus mucosa	UBERON:0035834	85.41	gold quality
placenta	UBERON:0001987	84.41	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.26	gold quality
upper leg skin	UBERON:0004262	84.01	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.78	gold quality
small intestine	UBERON:0002108	83.34	gold quality
right uterine tube	UBERON:0001302	83.12	gold quality
upper arm skin	UBERON:0004263	83.03	gold quality
skin of hip	UBERON:0001554	82.81	gold quality
rectum	UBERON:0001052	82.76	gold quality
germinal epithelium of ovary	UBERON:0001304	82.69	gold quality
palpebral conjunctiva	UBERON:0001812	82.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

59 targeting ZNF600, 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-3064-3P	100.00	70.09	1254
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-106A-3P	99.53	67.58	995
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-19A-5P	99.36	66.93	1675

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 600 — Q6ZNG1 (reviewed: Q6ZNG1)

All UniProt accessions (4): A0A3B3IT03, A0A3B3ITH4, A0A3B3ITY9, Q6ZNG1

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 (3): NP_001308795, NP_001308796, NP_940859 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily

Pfam: PF00096, PF12874

UniProt features (26 total): zinc finger region 20, sequence variant 3, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNG1-F1	68.20	0.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 91 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, PEREZ_TP63_TARGETS, PEREZ_TP53_AND_TP63_TARGETS, NOUZOVA_TRETINOIN_AND_H4_ACETYLATION, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, ARNT2_TARGET_GENES, HMG20B_TARGET_GENES, PAX7_TARGET_GENES, ZNF768_TARGET_GENES, MIR616_5P, MIR371B_5P, MIR373_5P

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355), regulation of gene expression (GO:0010468), negative regulation of macromolecule biosynthetic process (GO:0010558)

GO Molecular Function (4): DNA binding (GO:0003677), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

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 macromolecule biosynthetic process	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
gene expression	1
macromolecule biosynthetic process	1
negative regulation of biosynthetic process	1
negative regulation of macromolecule metabolic process	1
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

380 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF600	NBPF26	B4DH59	507
ZNF600	A6NLF2	A6NLF2	506
ZNF600	A0A087WTG0	A0A087WTG0	506
ZNF600	TTC33	Q6PID6	378
ZNF600	TMEM217B	A0A494BZU4	369
ZNF600	TMEM217	Q8N7C4	367
ZNF600	Q8NG57	Q8NG57	335
ZNF600	VPS13B	Q7Z7G8	328
ZNF600	C9JR48	C9JR48	322
ZNF600	ACOT6	Q3I5F7	320
ZNF600	LRRC37A2	A6NM11	317
ZNF600	ACTL8	Q9H568	312
ZNF600	PPWD1	Q96BP3	305
ZNF600	CARF	Q8N187	305
ZNF600	RAD9B	Q6WBX8	278

IntAct

6 interactions, top by confidence:

A	B	Type	Score
KRTAP10-6	ZNF600	psi-mi:“MI:0915”(physical association)	0.560
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF600	KRTAP10-6	psi-mi:“MI:0915”(physical association)	0.000
MAPK6	ZNF600	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (4): ZNF600 (Two-hybrid), ZNF600 (Affinity Capture-MS), ZNF600 (Cross-Linking-MS (XL-MS)), ZNF600 (Two-hybrid)

ESM2 similar proteins: A6NDX5, A6NK75, A6NNF4, A6NP11, B4DXR9, B7Z6K7, C9JN71, O43361, O75290, O75373, P0CJ79, P0DKX0, P17019, P17021, P17035, P17039, P35789, Q02386, Q03938, Q08AN1, Q13106, Q15928, Q3ZCX4, Q5R9F0, Q5SXM1, Q68EA5, Q6P9A1, Q6PDB4, Q6ZN06, Q6ZN08, Q6ZNG1, Q76KX8, Q86V71, Q86XN6, Q8IYB9, Q8N4W9, Q8NEP9, Q8TBZ8, Q8TC21, Q8TF32

Diamond homologs: A0A1W2PQL4, A2RRD8, A2VDQ7, A6NHJ4, A6NK75, A6NN14, A6NNF4, A6NP11, B4DX44, B4DXR9, E9PW05, O14628, O43345, O75290, O75346, O75373, O75820, P0CB33, P0CJ79, P0DKX0, P10755, P17032, P17035, P52738, Q02386, Q03923, Q03936, Q05481, Q08AN1, Q09FC8, Q0VGE8, Q14586, Q14593, Q147U1, Q15928, Q3MIS6, Q3SXZ3, Q494X3, Q4R6C2, Q5HY98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	128
Likely benign	13
Benign	10

Top pathogenic / likely-pathogenic (0)

SpliceAI

768 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52778914:G:C	acceptor_gain	1.0000
19:52767770:TAT:T	acceptor_gain	0.9900
19:52774614:C:A	donor_gain	0.9900
19:52778816:A:AC	donor_gain	0.9900
19:52778853:T:A	donor_gain	0.9900
19:52778903:CAATC:C	acceptor_gain	0.9900
19:52778906:TC:T	acceptor_gain	0.9900
19:52778906:TCC:T	acceptor_loss	0.9900
19:52778907:CC:C	acceptor_gain	0.9900
19:52778908:C:CA	acceptor_loss	0.9900
19:52778908:C:CC	acceptor_gain	0.9900
19:52778912:A:C	acceptor_gain	0.9900
19:52778914:G:GC	acceptor_gain	0.9900
19:52786582:T:TA	donor_gain	0.9900
19:52786589:TCTTA:T	donor_loss	0.9900
19:52786590:CTTA:C	donor_loss	0.9900
19:52786591:TTA:T	donor_loss	0.9900
19:52786592:TACC:T	donor_loss	0.9900
19:52786593:A:AC	donor_gain	0.9900
19:52786593:A:AG	donor_loss	0.9900
19:52786594:C:CC	donor_gain	0.9900
19:52767768:GATAT:G	acceptor_gain	0.9800
19:52767772:TC:T	acceptor_loss	0.9800
19:52767773:C:CA	acceptor_loss	0.9800
19:52767773:C:CC	acceptor_gain	0.9800
19:52767774:T:C	acceptor_loss	0.9800
19:52778820:CTTCA:C	donor_loss	0.9800
19:52778822:T:TA	donor_gain	0.9800
19:52778822:TCA:T	donor_loss	0.9800
19:52778823:CAC:C	donor_loss	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000023557 (19:52797426 A>C), RS1000077423 (19:52797694 A>C,T), RS1000097013 (19:52798556 T>C), RS1000150928 (19:52798254 C>T), RS1000188220 (19:52774441 C>A,T), RS1000219757 (19:52828246 T>A), RS1000239116 (19:52768404 C>T), RS1000322919 (19:52764699 A>G), RS1000433727 (19:52788856 T>C), RS1000457592 (19:52823011 A>C), RS1000495693 (19:52769558 A>G), RS1000551525 (19:52783179 T>G), RS1000606465 (19:52829039 T>C), RS1000610410 (19:52794789 G>A), RS1000681844 (19:52793974 T>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

3 associations (top):

Study	Trait	p-value
GCST001414_11	Phospholipid levels (plasma)	9.000000e-09
GCST006479_21	Diverticular disease	8.000000e-06
GCST008477_3	Emphysema annual change measurement in smokers (adjusted lung density)	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0009959	diverticular disease
EFO:0007626	emphysema imaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	6
trichostatin A	affects cotreatment, increases expression	3
Aflatoxin B1	affects expression, increases expression, increases methylation	3
entinostat	affects cotreatment, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	increases expression	2
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methapyrilene	decreases methylation	1
Quercetin	increases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
1-Methyl-4-phenylpyridinium	increases expression	1
Cadmium Chloride	decreases expression	1
Lactic Acid	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_HD32	HEK293 eGFP-ZNF600	Transformed cell line	Female

Clinical trials (associated diseases)

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