ZNF611

Summary

ZNF611 (zinc finger protein 611, HGNC:28766) is a protein-coding gene on chromosome 19q13.41, encoding Zinc finger protein 611 (Q8N823). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-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 81856 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 155 total
• MANE Select transcript: NM_001161499

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28766
Approved symbol	ZNF611
Name	zinc finger protein 611
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	MGC5384
Ensembl gene	ENSG00000213020
Ensembl biotype	protein_coding
Entrez	81856

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 16 protein_coding, 5 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000319783, ENST00000453741, ENST00000540744, ENST00000543227, ENST00000595001, ENST00000595798, ENST00000596702, ENST00000596776, ENST00000597343, ENST00000597566, ENST00000598639, ENST00000598723, ENST00000599798, ENST00000600943, ENST00000601249, ENST00000601447, ENST00000601643, ENST00000602046, ENST00000602162, ENST00000640952, ENST00000652185, ENST00000886282, ENST00000886283, ENST00000937953, ENST00000949805, ENST00000949806

RefSeq mRNA: 4 — MANE Select: NM_001161499 NM_001161499, NM_001161500, NM_001161501, NM_030972

CCDS: CCDS12855, CCDS54312

Canonical transcript exons

ENST00000652185 — 6 exons

Exon	Start	End
ENSE00002220640	52729906	52730005
ENSE00002466154	52728730	52728831
ENSE00002508476	52735001	52735044
ENSE00003626048	52715832	52715913
ENSE00003891768	52714015	52714141
ENSE00003892451	52702813	52706864

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 99.35.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.3169 / max 57.4145, expressed in 1383 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182532	3.1219	1350
182531	0.1950	93

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	99.35	gold quality
renal medulla	UBERON:0000362	96.95	gold quality
blood vessel layer	UBERON:0004797	96.72	gold quality
sperm	CL:0000019	96.53	gold quality
cardia of stomach	UBERON:0001162	96.13	silver quality
ventral tegmental area	UBERON:0002691	96.03	gold quality
nipple	UBERON:0002030	95.81	gold quality
male germ cell	CL:0000015	95.73	gold quality
endothelial cell	CL:0000115	95.71	gold quality
tendon of biceps brachii	UBERON:0008188	95.43	gold quality
lateral globus pallidus	UBERON:0002476	95.24	silver quality
trigeminal ganglion	UBERON:0001675	95.20	gold quality
subthalamic nucleus	UBERON:0001906	95.19	silver quality
pylorus	UBERON:0001166	95.15	silver quality
superior surface of tongue	UBERON:0007371	95.04	gold quality
inferior vagus X ganglion	UBERON:0005363	94.99	gold quality
trachea	UBERON:0003126	94.46	silver quality
superior vestibular nucleus	UBERON:0007227	94.42	gold quality
dorsal plus ventral thalamus	UBERON:0001897	94.37	silver quality
substantia nigra pars compacta	UBERON:0001965	94.32	silver quality
dorsal root ganglion	UBERON:0000044	94.24	gold quality
periodontal ligament	UBERON:0008266	94.23	gold quality
vena cava	UBERON:0004087	94.17	gold quality
superficial temporal artery	UBERON:0001614	94.09	silver quality
substantia nigra pars reticulata	UBERON:0001966	94.09	silver quality
pericardium	UBERON:0002407	93.94	gold quality
visceral pleura	UBERON:0002401	93.91	gold quality
medulla oblongata	UBERON:0001896	93.76	gold quality
pons	UBERON:0000988	93.63	gold quality
lateral nuclear group of thalamus	UBERON:0002736	93.58	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-106540	no	146.13
E-MTAB-10137	no	81.06
E-ANND-3	no	5.55

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

74 targeting ZNF611, 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-3925-3P	100.00	69.95	1237
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-6873-3P	100.00	71.42	2626
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-8068	99.98	73.85	2376
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-3658	99.96	73.87	4379
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-95-5P	99.89	72.17	3973
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107

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 611 — Q8N823 (reviewed: Q8N823)

All UniProt accessions (8): A0A1W2PQH1, Q8N823, M0QXE4, M0QXQ6, M0QYR0, M0QYZ5, M0R1T1, M0R2W3

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?
Q8N823-1	1	yes
Q8N823-2	2

RefSeq proteins (4): NP_001154971, NP_001154972, NP_001154973, NP_112234 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (29 total): zinc finger region 17, sequence variant 5, cross-link 2, sequence conflict 2, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N823-F1	64.55	0.01

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 173, 221

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 57 (showing top): RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, LIU_COMMON_CANCER_GENES, HAMAI_APOPTOSIS_VIA_TRAIL_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LU_EZH2_TARGETS_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ARID5B_TARGET_GENES, ASH1L_TARGET_GENES, ELF2_TARGET_GENES, SALL4_TARGET_GENES, ZNF350_TARGET_GENES, ZNF768_TARGET_GENES, MIR616_5P

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), positive regulation of DNA-templated transcription (GO:0045893), 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), zinc ion binding (GO:0008270), DNA binding (GO:0003677), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (2): nucleus (GO:0005634), chromosome (GO:0005694)

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	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
positive regulation of RNA biosynthetic process	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
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
DNA binding	1
cation binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

608 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF611	OR5AP2	Q8NGF4	475
ZNF611	RPP38	P78345	465
ZNF611	NXPE3	Q969Y0	455
ZNF611	FOXD4L6	Q3SYB3	448
ZNF611	OR1L8	Q8NGR8	445
ZNF611	OR8B4	Q96RC9	432
ZNF611	HORMAD1	Q86X24	422
ZNF611	OR5H14	A6NHG9	419
ZNF611	FBXO48	Q5FWF7	400
ZNF611	OR2I1	Q8NGU4	391
ZNF611	NOX5	Q96PH1	390
ZNF611	NUP62CL	Q9H1M0	376
ZNF611	THOC5	Q13769	374
ZNF611	RSPH10B	P0C881	368
ZNF611	OR4D10	Q8NGI6	368

IntAct

11 interactions, top by confidence:

A	B	Type	Score
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF611	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
ZNF611	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
ZNF611	H2AC4	psi-mi:“MI:0915”(physical association)	0.400
KLF8		psi-mi:“MI:0914”(association)	0.350
ZNF611	IPO8	psi-mi:“MI:0914”(association)	0.350
MAGEA9	CIBAR1	psi-mi:“MI:0914”(association)	0.350
NOTCH2	ZNF320	psi-mi:“MI:0914”(association)	0.350
LTBP2	ZNF320	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): ZNF611 (Affinity Capture-RNA), ZNF611 (Affinity Capture-MS), ZNF611 (Proximity Label-MS), ZNF611 (Proximity Label-MS), HIST1H2BH (Proximity Label-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-MS), ZNF611 (Affinity Capture-RNA)

ESM2 similar proteins: A2RRD8, A6NHJ4, B4DX44, O75346, P10077, P10755, P15621, P16372, P16373, P51786, P52737, P85977, Q0VGE8, Q14588, Q147U1, Q15928, Q15973, Q2M3X9, Q3KNS6, Q3MIS6, Q494X3, Q5HY98, Q5RBQ3, Q5REK1, Q5VIY5, Q60585, Q61751, Q6GQR8, Q7L2R6, Q7TSH9, Q8IYX0, Q8N782, Q8N823, Q8N988, Q8N9F8, Q8NA42, Q8NCK3, Q8NDP4, Q8NEP9, Q8TC21

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	132
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1256 predictions. Top by Δscore:

Variant	Effect	Δscore
19:52714008:T:A	donor_gain	1.0000
19:52714017:ACAG:A	donor_gain	1.0000
19:52714018:CAGC:C	donor_gain	1.0000
19:52714053:T:TA	donor_gain	1.0000
19:52714054:C:A	donor_gain	1.0000
19:52715911:ATCC:A	acceptor_loss	1.0000
19:52715912:TC:T	acceptor_gain	1.0000
19:52715912:TCCT:T	acceptor_loss	1.0000
19:52715913:CC:C	acceptor_gain	1.0000
19:52715914:C:CA	acceptor_loss	1.0000
19:52715915:T:C	acceptor_loss	1.0000
19:52715918:A:C	acceptor_gain	1.0000
19:52715920:G:C	acceptor_gain	1.0000
19:52715920:G:GC	acceptor_gain	1.0000
19:52715822:A:AC	donor_gain	0.9900
19:52715828:T:TA	donor_gain	0.9900
19:52715859:T:A	donor_gain	0.9900
19:52715909:CAATC:C	acceptor_gain	0.9900
19:52715910:AATC:A	acceptor_gain	0.9900
19:52715914:C:CC	acceptor_gain	0.9900
19:52715918:A:AC	acceptor_gain	0.9900
19:52730008:G:C	acceptor_gain	0.9900
19:52734997:TCA:T	donor_loss	0.9900
19:52734998:CACC:C	donor_loss	0.9900
19:52734999:ACC:A	donor_loss	0.9900
19:52735000:C:CG	donor_loss	0.9900
19:52706862:TAT:T	acceptor_gain	0.9800
19:52713986:C:CA	donor_gain	0.9800
19:52714013:AC:A	donor_gain	0.9800
19:52714014:CC:C	donor_gain	0.9800

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000010703 (19:52713600 A>C), RS1000029874 (19:52734911 T>C,G), RS1000035996 (19:52734130 A>G), RS1000063247 (19:52713800 A>G), RS1000111104 (19:52733167 G>A,C), RS1000120412 (19:52708978 T>C), RS1000208092 (19:52725567 G>C), RS1000243368 (19:52709202 A>C), RS1000496112 (19:52730962 G>A,C), RS1000551871 (19:52726230 C>T), RS1000614550 (19:52705001 T>C), RS1000654693 (19:52735211 C>T), RS1000720933 (19:52734410 G>A), RS1000722284 (19:52720329 G>A), RS1000775997 (19:52729901 C>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:300143

GenCC curated gene-disease

Mondo (1): intellectual disability, X-linked 21 (MONDO:0010256)

Orphanet (1): X-linked non-syndromic intellectual disability (Orphanet:777)

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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	decreases expression	2
Aflatoxin B1	increases methylation	2
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
geraniol	increases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Doxorubicin	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Formaldehyde	increases expression	1
Naphthoquinones	increases expression	1
Niclosamide	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Tetrachlorodibenzodioxin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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