ZNF549

Summary

ZNF549 (zinc finger protein 549, HGNC:26632) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 549 (Q6P9A3). 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 256051 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 91 total
• MANE Select transcript: NM_001199295

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26632
Approved symbol	ZNF549
Name	zinc finger protein 549
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	FLJ34917
Ensembl gene	ENSG00000121406
Ensembl biotype	protein_coding
OMIM	620720
Entrez	256051

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000240719, ENST00000376233, ENST00000594943, ENST00000602149, ENST00000928259

RefSeq mRNA: 2 — MANE Select: NM_001199295 NM_001199295, NM_153263

CCDS: CCDS12952, CCDS56106

Canonical transcript exons

ENST00000376233 — 4 exons

Exon	Start	End
ENSE00001267326	57527356	57527606
ENSE00001469833	57531070	57531108
ENSE00002450570	57535144	57535270
ENSE00003102124	57537204	57540876

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 86.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.4490 / max 39.1542, expressed in 1333 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177780	3.4490	1333

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.68	gold quality
cortical plate	UBERON:0005343	82.86	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.14	gold quality
cerebellar hemisphere	UBERON:0002245	78.97	gold quality
cerebellar cortex	UBERON:0002129	78.76	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.61	gold quality
ganglionic eminence	UBERON:0004023	78.16	gold quality
ventricular zone	UBERON:0003053	76.05	gold quality
calcaneal tendon	UBERON:0003701	75.93	gold quality
cerebellum	UBERON:0002037	75.20	gold quality
stromal cell of endometrium	CL:0002255	74.73	gold quality
granulocyte	CL:0000094	74.59	gold quality
apex of heart	UBERON:0002098	74.36	gold quality
right ovary	UBERON:0002118	73.91	gold quality
secondary oocyte	CL:0000655	73.61	silver quality
left ovary	UBERON:0002119	73.61	gold quality
islet of Langerhans	UBERON:0000006	73.12	gold quality
right lobe of thyroid gland	UBERON:0001119	72.84	gold quality
adenohypophysis	UBERON:0002196	72.53	gold quality
lower esophagus muscularis layer	UBERON:0035833	72.37	gold quality
lower esophagus	UBERON:0013473	72.33	gold quality
right adrenal gland cortex	UBERON:0035827	72.27	gold quality
gastrocnemius	UBERON:0001388	72.26	gold quality
right adrenal gland	UBERON:0001233	72.25	gold quality
muscle of leg	UBERON:0001383	72.10	gold quality
left lobe of thyroid gland	UBERON:0001120	72.07	gold quality
right uterine tube	UBERON:0001302	72.06	gold quality
descending thoracic aorta	UBERON:0002345	72.02	gold quality
left adrenal gland	UBERON:0001234	71.99	gold quality
right coronary artery	UBERON:0001625	71.98	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.98

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA1728.1	ZNF549	More than 3 adjacent zinc fingers
MA1728.2	ZNF549	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:27852650

miRNA regulators (miRDB)

67 targeting ZNF549, 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-8485	100.00	77.57	4731
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-4795-3P	100.00	74.62	4024
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-6888-3P	99.97	65.95	1170
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-4677-5P	99.70	70.09	1940
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-4527	99.66	67.43	714
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-6073	99.60	70.36	793
HSA-MIR-190A-5P	99.54	71.45	933

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfx	ENSDARG00000074453
danio_rerio		ENSDARG00000098424
mus_musculus	Zfy2	ENSMUSG00000000103
mus_musculus	Zfy1	ENSMUSG00000053211
rattus_norvegicus	Zfy1	ENSRNOG00000053042

Paralogs (38): ZFX (ENSG00000005889), ZBTB11 (ENSG00000066422), ZFAT (ENSG00000066827), ZFY (ENSG00000067646), ZNF586 (ENSG00000083828), IKZF5 (ENSG00000095574), ZNF419 (ENSG00000105136), ZSCAN20 (ENSG00000121903), ZNF304 (ENSG00000131845), PRDM15 (ENSG00000141956), ZNF660 (ENSG00000144792), ZNF711 (ENSG00000147180), ZNF773 (ENSG00000152439), ZNF256 (ENSG00000152454), ZNF837 (ENSG00000152475), ZNF691 (ENSG00000164011), ZNF610 (ENSG00000167554), E4F1 (ENSG00000167967), ZNF562 (ENSG00000171466), ZNF561 (ENSG00000171469), ZNF584 (ENSG00000171574), ZIK1 (ENSG00000171649), ZNF570 (ENSG00000171827), ZSCAN2 (ENSG00000176371), ZNF552 (ENSG00000178935), ZNF154 (ENSG00000179909), ZNF792 (ENSG00000180884), ZNF793 (ENSG00000188227), ZNF548 (ENSG00000188785), ZNF79 (ENSG00000196152), ZNF418 (ENSG00000196724), ZNF772 (ENSG00000197128), ZNF583 (ENSG00000198440), ZNF480 (ENSG00000198464), ZNF551 (ENSG00000204519), ZNF134 (ENSG00000213762), ZNF587B (ENSG00000269343), ZNF8 (ENSG00000278129)

Protein

Protein identifiers

Zinc finger protein 549 — Q6P9A3 (reviewed: Q6P9A3)

All UniProt accessions (3): Q6P9A3, M0QXN3, M0R0L6

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?
Q6P9A3-1	1	yes
Q6P9A3-2	2

RefSeq proteins (2): NP_001186224, NP_694995 (=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

Pfam: PF00096, PF01352

UniProt features (21 total): zinc finger region 15, chain 1, domain 1, cross-link 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P9A3-F1	65.21	0.17

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 (1): 223

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 42 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, LU_EZH2_TARGETS_DN, MYC_UP.V1_UP, JNK_DN.V1_DN, PTEN_DN.V2_UP, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ZNF257_TARGET_GENES, ZNF561_TARGET_GENES, MIR8485, MIR4755_5P, MIR5006_3P, MIR3119, MIR7_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 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), 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
RNA polymerase II transcription regulatory region sequence-specific DNA binding	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
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
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

628 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF549	SHISA3	A0PJX4	481
ZNF549	FZD3	Q9NPG1	428
ZNF549	FZD9	O00144	421
ZNF549	FGGY	Q96C11	420
ZNF549	RERG	Q96A58	399
ZNF549	WFDC10B	Q8IUB3	396
ZNF549	ANAPC11	Q9NYG5	386
ZNF549	TSPAN9	O75954	380
ZNF549	JHY	Q6NUN7	370
ZNF549	R3HCC1	Q9Y3T6	348
ZNF549	CRACDL	Q6NV74	348
ZNF549	RBM22	Q9NW64	346
ZNF549	UBAP1	Q9NZ09	342
ZNF549	LMAN1L	Q9HAT1	328
ZNF549	C11orf21	Q9P2W6	322

IntAct

8 interactions, top by confidence:

A	B	Type	Score
EMD	ZNF549	psi-mi:“MI:0915”(physical association)	0.560
ZNF549	SORL1	psi-mi:“MI:0915”(physical association)	0.400
IL3	ZNF549	psi-mi:“MI:0915”(physical association)	0.370
	ZNF549	psi-mi:“MI:0915”(physical association)	0.370
ZNF549	IPO8	psi-mi:“MI:0914”(association)	0.350
EMD	ZNF549	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): SORL1 (Affinity Capture-MS), ZNF549 (Two-hybrid), SORL1 (Affinity Capture-MS), ZNF549 (Affinity Capture-MS), ZNF549 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A6QLU5, B2RUI1, D3ZVT0, O14709, O43296, O75123, P10072, P15621, P17020, P17097, P51814, P85977, Q08ER8, Q0VGE8, Q14590, Q32KN0, Q3KQV3, Q4V8A8, Q5CZA5, Q5RBX0, Q5RCD9, Q5VIY5, Q61116, Q61967, Q6GQR8, Q6P9A3, Q6ZMS4, Q7TSH9, Q7TSI0, Q7Z3I7, Q86UD4, Q86WZ6, Q8BFS8, Q8IZ26, Q8N9F8, Q8TAF7

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	85
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1356 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57529003:G:GA	donor_gain	1.0000
19:57556225:CATTA:C	donor_loss	1.0000
19:57556226:ATTAC:A	donor_loss	1.0000
19:57556228:TACC:T	donor_loss	1.0000
19:57556229:A:C	donor_loss	1.0000
19:57556353:AACAT:A	acceptor_gain	1.0000
19:57556354:ACAT:A	acceptor_gain	1.0000
19:57556355:CAT:C	acceptor_gain	1.0000
19:57556355:CATC:C	acceptor_gain	1.0000
19:57556356:AT:A	acceptor_gain	1.0000
19:57556356:ATCTG:A	acceptor_loss	1.0000
19:57556358:C:CC	acceptor_gain	1.0000
19:57556358:CT:C	acceptor_loss	1.0000
19:57529002:T:TA	donor_gain	0.9900
19:57544457:AGGG:A	donor_gain	0.9900
19:57544503:T:TA	donor_gain	0.9900
19:57552621:GCTTA:G	donor_loss	0.9900
19:57552622:CTTA:C	donor_loss	0.9900
19:57552624:TACCT:T	donor_loss	0.9900
19:57552625:A:AT	donor_loss	0.9900
19:57552719:TGCC:T	acceptor_gain	0.9900
19:57556359:T:A	acceptor_loss	0.9900
19:57556367:C:CT	acceptor_gain	0.9900
19:57552719:TGCCC:T	acceptor_loss	0.9800
19:57552720:GCCCT:G	acceptor_loss	0.9800
19:57552721:CC:C	acceptor_gain	0.9800
19:57552722:CC:C	acceptor_gain	0.9800
19:57552723:C:CC	acceptor_gain	0.9800
19:57552723:CTGTT:C	acceptor_loss	0.9800
19:57552724:T:A	acceptor_loss	0.9800

AlphaMissense

4274 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57538784:T:C	F594L	0.999
19:57538786:T:A	F594L	0.999
19:57538786:T:G	F594L	0.999
19:57538868:T:C	F622L	0.999
19:57538870:C:A	F622L	0.999
19:57538870:C:G	F622L	0.999
19:57538700:T:C	F566L	0.998
19:57538702:T:A	F566L	0.998
19:57538702:T:G	F566L	0.998
19:57538280:T:C	F426L	0.997
19:57538282:C:A	F426L	0.997
19:57538282:C:G	F426L	0.997
19:57538448:T:C	F482L	0.997
19:57538450:C:A	F482L	0.997
19:57538450:C:G	F482L	0.997
19:57538818:G:C	R605P	0.997
19:57538813:T:A	H603Q	0.996
19:57538813:T:G	H603Q	0.996
19:57538364:T:C	F454L	0.995
19:57538366:T:A	F454L	0.995
19:57538366:T:G	F454L	0.995
19:57538371:G:C	R456P	0.995
19:57538729:C:A	H575Q	0.995
19:57538729:C:G	H575Q	0.995
19:57538815:A:C	Q604P	0.995
19:57538321:T:A	H439Q	0.994
19:57538321:T:G	H439Q	0.994
19:57538727:C:G	H575D	0.994
19:57538731:A:C	Q576P	0.994
19:57538785:T:C	F594S	0.994

dbSNP variants (sampled 300 via entrez): RS1000127514 (19:57527355 C>A,G), RS1000444697 (19:57530461 C>T), RS1000516342 (19:57530037 G>A), RS1000547408 (19:57530244 G>C), RS1000724662 (19:57536282 A>G,T), RS1000903663 (19:57536401 G>A,T), RS1001259718 (19:57529867 C>A,T), RS1001316246 (19:57529834 C>T), RS1001370288 (19:57540177 A>G), RS1001382743 (19:57535734 A>T), RS1001383854 (19:57533507 G>T), RS1001416703 (19:57533816 T>C), RS1002052094 (19:57539933 G>A,C), RS1002150595 (19:57525689 T>C), RS1002187277 (19:57528677 A>G)

Disease associations

OMIM: gene MIM:620720 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

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

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	increases abundance, increases expression, affects cotreatment	2
bisphenol F	affects cotreatment, increases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
terbufos	increases methylation	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
chloropicrin	increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Fonofos	increases methylation	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	increases expression, affects cotreatment	1

Clinical trials (associated diseases)

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