ZNF544

Summary

ZNF544 (zinc finger protein 544, HGNC:16759) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 544 (Q6NX49). 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 27300 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 143 total
• MANE Select transcript: NM_014480

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16759
Approved symbol	ZNF544
Name	zinc finger protein 544
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	AF020591
Ensembl gene	ENSG00000198131
Ensembl biotype	protein_coding
Entrez	27300

Gene structure

Transcript identifiers

Ensembl transcripts: 38 — 29 protein_coding, 7 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000269829, ENST00000594303, ENST00000594384, ENST00000595981, ENST00000596597, ENST00000596652, ENST00000596677, ENST00000596825, ENST00000596929, ENST00000597240, ENST00000597564, ENST00000598880, ENST00000599227, ENST00000599714, ENST00000599953, ENST00000600044, ENST00000600220, ENST00000600775, ENST00000602260, ENST00000627781, ENST00000651034, ENST00000652201, ENST00000687789, ENST00000853338, ENST00000853339, ENST00000853340, ENST00000853341, ENST00000853342, ENST00000853343, ENST00000853344, ENST00000914894, ENST00000914895, ENST00000914896, ENST00000914897, ENST00000914898, ENST00000914899, ENST00000942565, ENST00000942566

RefSeq mRNA: 60 — MANE Select: NM_014480 NM_001320767, NM_001320769, NM_001320770, NM_001320771, NM_001320773, NM_001320774, NM_001320776, NM_001320777, NM_001320780, NM_001320781, NM_001320782, NM_001320783, NM_001320785, NM_001320786, NM_001320787, NM_001320788, NM_001320789, NM_001320791, NM_001320792, NM_001387390, NM_001387391, NM_001387392, NM_001387393, NM_001387394, NM_001387395, NM_001387396, NM_001387397, NM_001387398, NM_001387399, NM_001387400, NM_001387401, NM_001387402, NM_001387403, NM_001387407, NM_001387408, NM_001387409, NM_001387410, NM_001387413, NM_001387415, NM_001387416, NM_001387417, NM_001387418, NM_001387419, NM_001387420, NM_001387421, NM_001387422, NM_001387423, NM_001387424, NM_001387425, NM_001387426, NM_001387427, NM_001387428, NM_001387429, NM_001387431, NM_001387432, NM_001387433, NM_001387434, NM_001387435, NM_001387436, NM_014480

CCDS: CCDS12973, CCDS82411, CCDS82412, CCDS82413, CCDS92700, CCDS92701

Canonical transcript exons

ENST00000687789 — 7 exons

Exon	Start	End
ENSE00001555822	58230394	58230462
ENSE00001564064	58229468	58229570
ENSE00002984539	58228914	58228946
ENSE00003488886	58243965	58244056
ENSE00003504651	58246711	58246794
ENSE00003661832	58246301	58246427
ENSE00003928379	58260851	58263644

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 93.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.5307 / max 91.0908, expressed in 1689 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177820	7.1912	1683
177821	0.3396	161

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	93.99	silver quality
endothelial cell	CL:0000115	92.38	gold quality
cervix squamous epithelium	UBERON:0006922	91.79	gold quality
ventricular zone	UBERON:0003053	90.66	gold quality
tendon of biceps brachii	UBERON:0008188	90.56	silver quality
sperm	CL:0000019	89.86	gold quality
ganglionic eminence	UBERON:0004023	89.47	gold quality
right uterine tube	UBERON:0001302	89.15	gold quality
right testis	UBERON:0004534	89.02	gold quality
left testis	UBERON:0004533	89.00	gold quality
male germ cell	CL:0000015	88.62	gold quality
adenohypophysis	UBERON:0002196	87.83	gold quality
testis	UBERON:0000473	87.77	gold quality
gingival epithelium	UBERON:0001949	87.68	gold quality
adrenal tissue	UBERON:0018303	87.67	gold quality
apex of heart	UBERON:0002098	87.62	gold quality
amniotic fluid	UBERON:0000173	87.61	gold quality
pituitary gland	UBERON:0000007	87.58	gold quality
cerebellar cortex	UBERON:0002129	87.34	gold quality
cerebellar hemisphere	UBERON:0002245	87.31	gold quality
right lobe of thyroid gland	UBERON:0001119	87.29	gold quality
hair follicle	UBERON:0002073	87.22	gold quality
cortical plate	UBERON:0005343	87.13	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.12	gold quality
thyroid gland	UBERON:0002046	86.95	gold quality
tonsil	UBERON:0002372	86.93	gold quality
cerebellum	UBERON:0002037	86.91	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.90	gold quality
squamous epithelium	UBERON:0006914	86.88	gold quality
embryo	UBERON:0000922	86.83	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.96
E-MTAB-5061	no	2.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting ZNF544, 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-188-3P	100.00	68.76	1240
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-3156-3P	99.76	66.72	939
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-543	99.52	69.03	2595
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-653-5P	99.46	67.35	1300
HSA-MIR-5589-3P	99.29	68.30	1443
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-5587-5P	99.07	68.58	838
HSA-MIR-376A-3P	99.06	69.17	1128
HSA-MIR-376B-3P	99.06	69.17	1128
HSA-MIR-628-3P	99.04	68.37	814
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-487A-5P	98.85	69.37	993
HSA-MIR-487B-5P	98.85	69.48	987
HSA-MIR-548Q	98.71	65.35	563
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-12125	98.59	67.54	1044

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 544 — Q6NX49 (reviewed: Q6NX49)

All UniProt accessions (9): Q6NX49, J3KQC8, M0QX86, M0QY11, M0QZM7, M0QZY0, M0R0U7, M0R2F0, Q8IVS5

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 (60): NP_001307696, NP_001307698, NP_001307699, NP_001307700, NP_001307702, NP_001307703, NP_001307705, NP_001307706, NP_001307709, NP_001307710, NP_001307711, NP_001307712, NP_001307714, NP_001307715, NP_001307716, NP_001307717, NP_001307718, NP_001307720, NP_001307721, NP_001374319, NP_001374320, NP_001374321, NP_001374322, NP_001374323, NP_001374324, NP_001374325, NP_001374326, NP_001374327, NP_001374328, NP_001374329, NP_001374330, NP_001374331, NP_001374332, NP_001374336, NP_001374337, NP_001374338, NP_001374339, NP_001374342, NP_001374344, NP_001374345, NP_001374346, NP_001374347, NP_001374348, NP_001374349, NP_001374350, NP_001374351, NP_001374352, NP_001374353, NP_001374354, NP_001374355, NP_001374356, NP_001374357, NP_001374358, NP_001374360, NP_001374361, NP_001374362, NP_001374363, NP_001374364, NP_001374365, NP_055295* (*=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
IPR056436	Znf-C2H2_ZIC1-5/GLI1-3-like	Domain

Pfam: PF00096, PF01352, PF23561

UniProt features (25 total): zinc finger region 13, sequence conflict 5, cross-link 3, sequence variant 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NX49-F1	63.40	0.25

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 (3): 273, 289, 534

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 114 (showing top): BLALOCK_ALZHEIMERS_DISEASE_UP, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, ACEVEDO_LIVER_CANCER_UP, DANG_BOUND_BY_MYC, OSMAN_BLADDER_CANCER_DN, MULLIGHAN_MLL_SIGNATURE_2_DN, NUYTTEN_EZH2_TARGETS_DN, CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, ONKEN_UVEAL_MELANOMA_DN, MTOR_UP.N4.V1_DN, FOXN3_TARGET_GENES, ZNF22_TARGET_GENES, ZNF711_TARGET_GENES

GO Biological Process (2): regulation of transcription by RNA polymerase II (GO:0006357), regulation of DNA-templated transcription (GO:0006355)

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 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
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

562 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF544	PEX2	P28328	411
ZNF544	TSTD2	Q5T7W7	400
ZNF544	ST3GAL3	Q11203	399
ZNF544	FAM32A	Q9Y421	348
ZNF544	PTCHD4	Q6ZW05	330
ZNF544	ALPK1	Q96QP1	324
ZNF544	SPATA31H1	Q68DN1	322
ZNF544	FAM124B	Q9H5Z6	306
ZNF544	SLC35E2A	P0CK97	305
ZNF544	DENND2A	Q9ULE3	296
ZNF544	SLC35E2B	P0CK96	292
ZNF544	DNMBP	Q6XZF7	291
ZNF544	AKR1E2	Q96JD6	290
ZNF544	ACP4	Q9BZG2	272
ZNF544	NOL8	Q76FK4	270

IntAct

23 interactions, top by confidence:

A	B	Type	Score
ZNF544	NDEL1	psi-mi:“MI:0915”(physical association)	0.740
NDEL1	ZNF544	psi-mi:“MI:0915”(physical association)	0.740
ZNF544	TRAF2	psi-mi:“MI:0915”(physical association)	0.670
TRAF2	ZNF544	psi-mi:“MI:0915”(physical association)	0.670
ZNF544	GLRX3	psi-mi:“MI:0915”(physical association)	0.560
TSGA10	ZNF544	psi-mi:“MI:0915”(physical association)	0.560
ZNF544	TSGA10	psi-mi:“MI:0915”(physical association)	0.560
ZNF544	GNPAT	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
ZNF544	HSPA8	psi-mi:“MI:0915”(physical association)	0.400
ZNF544	RABIF	psi-mi:“MI:0915”(physical association)	0.370
NDEL1	ZNF544	psi-mi:“MI:0915”(physical association)	0.000
	ZNF544	psi-mi:“MI:0915”(physical association)	0.000
ZNF544	recN	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): ZNF544 (Two-hybrid), ZNF544 (Two-hybrid), TSGA10 (Two-hybrid), NDEL1 (Two-hybrid), ZNF544 (Affinity Capture-RNA), ZNF544 (Affinity Capture-RNA), ZNF544 (Affinity Capture-RNA), RABIF (Two-hybrid), ZAK (Affinity Capture-MS), GNPAT (Affinity Capture-MS), CENPB (Affinity Capture-MS), ZNF544 (Affinity Capture-RNA), ZNF544 (Proximity Label-MS), ZNF544 (Affinity Capture-RNA), ZAK (Affinity Capture-MS)

ESM2 similar proteins: A0A087WUV0, A0JNB1, A2VDP4, B2RUI1, P0CG31, P10072, P17025, P17036, P17097, P18733, P51814, Q08ER8, Q09FC8, Q0VGE8, Q14590, Q15937, Q16600, Q2M3X9, Q4V8A8, Q5CZA5, Q5R8G9, Q5RBX0, Q5VIY5, Q68DI1, Q6J6I6, Q6NX49, Q6P1L6, Q6PG37, Q6ZMS4, Q6ZMW2, Q80YP6, Q86UD4, Q86Y25, Q8IZ26, Q8N184, Q8NB42, Q8NEK5, Q8TAF7, Q8TF47, Q8WXB4

Diamond homologs: A0JNB1, A1L1L7, A6NK53, A6QLU5, A6QPT6, A7MBI1, A8MQ14, A8MT65, B4DU55, O60765, P10076, P17014, P17098, P21506, P51523, P52742, P59923, P85977, Q06730, Q06732, Q08DG8, Q0VCB0, Q13360, Q14587, Q14590, Q147U1, Q16587, Q32M78, Q3KNS6, Q3MIS6, Q3V080, Q3ZCX4, Q4R6C2, Q4R6J4, Q4R882, Q4V8A8, Q4V8E9, Q571J5, Q5HY98, Q5JUW0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	124
Likely benign	10
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1706 predictions. Top by Δscore:

Variant	Effect	Δscore
19:58229567:AATGG:A	donor_loss	1.0000
19:58229568:ATG:A	donor_gain	1.0000
19:58229568:ATGG:A	donor_loss	1.0000
19:58229570:GGTA:G	donor_loss	1.0000
19:58229571:G:GA	donor_loss	1.0000
19:58229571:G:GG	donor_gain	1.0000
19:58229572:T:G	donor_loss	1.0000
19:58243959:C:G	acceptor_gain	1.0000
19:58243959:CCCCA:C	acceptor_loss	1.0000
19:58243960:CCCA:C	acceptor_loss	1.0000
19:58243960:CCCAG:C	acceptor_loss	1.0000
19:58243961:CCAGA:C	acceptor_loss	1.0000
19:58243962:CA:C	acceptor_loss	1.0000
19:58243963:A:AG	acceptor_gain	1.0000
19:58243963:AGAC:A	acceptor_loss	1.0000
19:58243963:AGACT:A	acceptor_gain	1.0000
19:58243964:G:GG	acceptor_gain	1.0000
19:58243964:GACT:G	acceptor_gain	1.0000
19:58243964:GACTG:G	acceptor_gain	1.0000
19:58246295:TTTCA:T	acceptor_loss	1.0000
19:58246296:TTCA:T	acceptor_loss	1.0000
19:58246298:CAGGC:C	acceptor_loss	1.0000
19:58246299:A:T	acceptor_loss	1.0000
19:58246300:G:A	acceptor_loss	1.0000
19:58246300:GGC:G	acceptor_gain	1.0000
19:58246300:GGCAT:G	acceptor_gain	1.0000
19:58246426:GG:G	donor_gain	1.0000
19:58246426:GGGT:G	donor_loss	1.0000
19:58246427:GG:G	donor_gain	1.0000
19:58246427:GGT:G	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000043873 (19:58270191 G>C), RS1000046687 (19:58266597 G>A), RS1000057571 (19:58228077 C>T), RS1000108186 (19:58273041 T>C,G), RS1000135441 (19:58260680 T>C), RS1000245578 (19:58244870 C>G,T), RS1000289380 (19:58277760 A>G), RS1000297937 (19:58244659 T>A,C,G), RS1000357720 (19:58239416 G>T), RS1000447438 (19:58257613 T>C), RS1000465051 (19:58263607 C>A,T), RS1000556170 (19:58237993 C>T), RS1000612219 (19:58264248 G>T), RS1000628021 (19:58227498 C>A,G), RS1000785010 (19:58250733 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

1 associations (top):

Study	Trait	p-value
GCST000281_15	Attention deficit hyperactivity disorder	8.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, increases methylation	2
aristolochic acid I	decreases expression	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
urushiol	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Temozolomide	increases expression	1
Adenine	decreases expression	1
Aldehydes	increases expression	1
Cisplatin	decreases expression	1
Colchicine	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	affects expression	1
Ethyl Methanesulfonate	decreases expression	1
Etoposide	decreases expression	1
Hydrogen Peroxide	affects expression	1
Hydroxyurea	decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Phthalic Acids	decreases expression	1
Silicon Dioxide	increases expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Mitomycin	decreases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases 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_XW61	HEK293 eGFP-ZNF544	Transformed cell line	Female

Clinical trials (associated diseases)

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