ZNF44

Summary

ZNF44 (zinc finger protein 44, HGNC:13110) is a protein-coding gene on chromosome 19p13.2, encoding Zinc finger protein 44 (P15621). 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 51710 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 100 total
• MANE Select transcript: NM_016264

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13110
Approved symbol	ZNF44
Name	zinc finger protein 44
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	KOX7, ZNF504
Ensembl gene	ENSG00000197857
Ensembl biotype	protein_coding
OMIM	194542
Entrez	51710

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 4 nonsense_mediated_decay, 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000354656, ENST00000355684, ENST00000356109, ENST00000393337, ENST00000397742, ENST00000483826, ENST00000597563, ENST00000600003, ENST00000697576, ENST00000854893

RefSeq mRNA: 7 — MANE Select: NM_016264 NM_001164276, NM_001353549, NM_001353550, NM_001353551, NM_001353552, NM_001353553, NM_016264

CCDS: CCDS45988, CCDS54223

Canonical transcript exons

ENST00000355684 — 4 exons

Exon	Start	End
ENSE00001484780	12294692	12294883
ENSE00001612532	12271808	12274063
ENSE00001675065	12274973	12275033
ENSE00003512422	12275956	12276082

Expression profiles

Bgee: expression breadth ubiquitous, 284 present calls, max score 97.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.6673 / max 105.4209, expressed in 1514 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179296	3.1080	1198
179295	2.0741	747
179297	1.0973	605
179294	0.3142	151
179293	0.0737	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	97.27	gold quality
renal medulla	UBERON:0000362	95.23	gold quality
blood vessel layer	UBERON:0004797	94.56	gold quality
pylorus	UBERON:0001166	93.88	gold quality
superficial temporal artery	UBERON:0001614	93.78	gold quality
cardia of stomach	UBERON:0001162	93.41	gold quality
mucosa of paranasal sinus	UBERON:0005030	93.38	gold quality
superior surface of tongue	UBERON:0007371	93.29	gold quality
visceral pleura	UBERON:0002401	93.26	gold quality
nipple	UBERON:0002030	93.14	gold quality
caput epididymis	UBERON:0004358	93.12	gold quality
oocyte	CL:0000023	93.03	gold quality
oral cavity	UBERON:0000167	92.85	gold quality
bronchial epithelial cell	CL:0002328	91.67	gold quality
jejunal mucosa	UBERON:0000399	91.61	gold quality
seminal vesicle	UBERON:0000998	91.33	gold quality
jejunum	UBERON:0002115	91.24	gold quality
pericardium	UBERON:0002407	90.83	gold quality
cauda epididymis	UBERON:0004360	90.76	gold quality
urethra	UBERON:0000057	90.52	gold quality
penis	UBERON:0000989	90.48	gold quality
inferior vagus X ganglion	UBERON:0005363	90.45	gold quality
trabecular bone tissue	UBERON:0002483	90.32	gold quality
corpus epididymis	UBERON:0004359	90.31	gold quality
endometrium epithelium	UBERON:0004811	90.29	gold quality
secondary oocyte	CL:0000655	90.24	gold quality
tibia	UBERON:0000979	90.24	gold quality
pharyngeal mucosa	UBERON:0000355	90.23	gold quality
trigeminal ganglion	UBERON:0001675	90.06	gold quality
synovial joint	UBERON:0002217	90.05	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	21.59
E-ANND-3	yes	6.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting ZNF44, 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-513A-5P	100.00	69.77	2465
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-520G-3P	98.91	67.38	1914
HSA-MIR-520H	98.91	67.38	1914
HSA-MIR-3145-3P	98.85	69.07	2031
HSA-MIR-7114-5P	98.51	67.87	1349
HSA-MIR-4768-3P	98.16	66.02	2330
HSA-MIR-4305	97.94	68.63	533
HSA-MIR-510-5P	97.66	65.82	916
HSA-MIR-4759	97.39	65.86	608
HSA-MIR-8056	97.15	64.49	769
HSA-MIR-3116	97.07	65.78	1324
HSA-MIR-552-3P	96.68	64.12	1026
HSA-MIR-3976	96.67	67.79	1187
HSA-MIR-331-5P	96.59	67.94	705

Literature-anchored findings (GeneRIF, showing 1)

• RNA-Sequencing Combined With Genome-Wide Allele-Specific Expression Patterning Identifies ZNF44 Variants as a Potential New Driver Gene for Pediatric Neuroblastoma. (PMID:37161925)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp961	ENSMUSG00000052446
rattus_norvegicus	Zfp617	ENSRNOG00000049856

Paralogs (15): ZNF14 (ENSG00000105708), ZNF57 (ENSG00000171970), ZNF791 (ENSG00000173875), ZNF443 (ENSG00000180855), ZNF101 (ENSG00000181896), ZNF563 (ENSG00000188868), ZNF799 (ENSG00000196466), ZNF700 (ENSG00000196757), ZNF441 (ENSG00000197044), ZNF433 (ENSG00000197647), ZNF823 (ENSG00000197933), ZNF442 (ENSG00000198342), ZNF844 (ENSG00000223547), ZNF709 (ENSG00000242852), ZNF878 (ENSG00000257446)

Protein

Protein identifiers

Zinc finger protein 44 — P15621 (reviewed: P15621)

Alternative names: Gonadotropin-inducible ovary transcription repressor 2, Zinc finger protein 55, Zinc finger protein 58, Zinc finger protein KOX7

All UniProt accessions (5): A0A8V8TMG8, E2QRP2, F8W7T7, M0R160, P15621

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 (3)

UniProt ID	Names	Canonical?
P15621-1	1	yes
P15621-2	2
P15621-3	3

RefSeq proteins (7): NP_001157748, NP_001340478, NP_001340479, NP_001340480, NP_001340481, NP_001340482, NP_057348* (*=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
IPR050826	Krueppel_C2H2_ZnFinger	Family

Pfam: PF00096, PF01352

UniProt features (25 total): zinc finger region 17, splice variant 3, sequence variant 2, chain 1, domain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P15621-F1	66.38	0.02

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): BROWNE_HCMV_INFECTION_6HR_DN, AAGCCAT_MIR135A_MIR135B, RODRIGUES_NTN1_TARGETS_DN, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP, DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP, FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, BROWNE_HCMV_INFECTION_14HR_UP, CHEN_HOXA5_TARGETS_9HR_UP, chr19p13, STEIN_ESRRA_TARGETS_UP, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, ACACTGG_MIR199A_MIR199B, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP, P53_DN.V1_UP

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of transcription by RNA polymerase II (GO:0000122), 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), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription by RNA polymerase II	2
regulation of transcription by RNA polymerase II	2
regulation of DNA-templated transcription	1
negative regulation of DNA-templated transcription	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
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2042 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF44	TRIM28	Q13263	981
ZNF44	ZUP1	Q96AP4	855
ZNF44	USP5	P45974	818
ZNF44	UBB	P02248	810
ZNF44	YOD1	Q5VVQ6	787
ZNF44	USP44	Q9H0E7	756
ZNF44	OTUD7A	Q8TE49	739
ZNF44	SETDB1	Q15047	689
ZNF44	ZPR1	O75312	670
ZNF44	CRBN	Q96SW2	660
ZNF44	HDAC6	Q9UBN7	653
ZNF44	UBA2	Q9UBT2	646
ZNF44	PHF20	Q9BVI0	638
ZNF44	NPLOC4	Q8TAT6	568
ZNF44	ZFAND5	O76080	558

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ZNF44	TRIM28	psi-mi:“MI:0914”(association)	0.350
ZNF44	ZNF195	psi-mi:“MI:0914”(association)	0.350
CSNK2B	ZNF44	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (23): RDH13 (Affinity Capture-MS), ZNF44 (Affinity Capture-RNA), ZNF44 (Affinity Capture-MS), ZNF44 (Two-hybrid), ZNF44 (Two-hybrid), ZNF44 (Affinity Capture-MS), RDH13 (Affinity Capture-MS), TRIM28 (Affinity Capture-MS), TRIB3 (Affinity Capture-MS), POGK (Affinity Capture-MS), THTPA (Affinity Capture-MS), ZNF195 (Affinity Capture-MS), TRIM33 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), GTF3C5 (Affinity Capture-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: A2VDP4, B7Z6K7, D3ZVT0, E7ETH6, E9Q8G5, O43296, O43361, O75290, O75467, O75820, P0CH99, P0CI00, P15621, P17021, P17023, P17024, P17030, P17032, P52740, P52741, Q02525, Q06732, Q08DG8, Q08ER8, Q0VCB0, Q13106, Q13398, Q14587, Q147U1, Q15935, Q2M218, Q2M3X9, Q32M78, Q3KQV3, Q3SY52, Q3V080, Q3ZCX4, Q4R882, Q4V8A8, Q5CZA5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	2
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1113 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12274059:CACAC:C	acceptor_gain	1.0000
19:12274061:CAC:C	acceptor_gain	1.0000
19:12274064:C:CC	acceptor_gain	1.0000
19:12274971:ACCT:A	donor_loss	1.0000
19:12274972:C:CG	donor_loss	1.0000
19:12275029:CATTC:C	acceptor_gain	1.0000
19:12275031:TTC:T	acceptor_gain	1.0000
19:12275032:TCCT:T	acceptor_loss	1.0000
19:12275034:C:A	acceptor_loss	1.0000
19:12275034:C:CC	acceptor_gain	1.0000
19:12275035:T:A	acceptor_loss	1.0000
19:12294687:CTCA:C	donor_loss	1.0000
19:12294688:TCA:T	donor_loss	1.0000
19:12294689:CA:C	donor_loss	1.0000
19:12294690:A:AT	donor_loss	1.0000
19:12274060:ACAC:A	acceptor_gain	0.9900
19:12274061:CACC:C	acceptor_gain	0.9900
19:12274062:AC:A	acceptor_gain	0.9900
19:12274063:CC:C	acceptor_gain	0.9900
19:12274065:T:A	acceptor_loss	0.9900
19:12275032:TC:T	acceptor_gain	0.9900
19:12275033:CC:C	acceptor_gain	0.9900
19:12276092:CCCA:C	acceptor_gain	0.9900
19:12276093:CCATA:C	acceptor_gain	0.9900
19:12276094:CATA:C	acceptor_gain	0.9900
19:12276095:A:C	acceptor_gain	0.9900
19:12276102:C:CT	acceptor_gain	0.9900
19:12276102:C:T	acceptor_gain	0.9900
19:12276103:A:T	acceptor_gain	0.9900
19:12291110:T:TA	donor_gain	0.9900

AlphaMissense

4126 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12273385:G:C	F338L	0.995
19:12273385:G:T	F338L	0.995
19:12273387:A:G	F338L	0.995
19:12273301:A:C	F366L	0.991
19:12273301:A:T	F366L	0.991
19:12273303:A:G	F366L	0.991
19:12273553:G:C	F282L	0.990
19:12273553:G:T	F282L	0.990
19:12273555:A:G	F282L	0.990
19:12272548:G:C	F617L	0.988
19:12272548:G:T	F617L	0.988
19:12272550:A:G	F617L	0.988
19:12272965:G:C	F478L	0.987
19:12272965:G:T	F478L	0.987
19:12272967:A:G	F478L	0.987
19:12276047:G:C	F61L	0.986
19:12276047:G:T	F61L	0.986
19:12276049:A:G	F61L	0.986
19:12276048:A:G	F61S	0.984
19:12273049:A:C	F450L	0.980
19:12273049:A:T	F450L	0.980
19:12273051:A:G	F450L	0.980
19:12272464:G:C	F645L	0.979
19:12272464:G:T	F645L	0.979
19:12272466:A:G	F645L	0.979
19:12273274:G:C	H375Q	0.978
19:12273274:G:T	H375Q	0.978
19:12273637:A:C	F254L	0.978
19:12273637:A:T	F254L	0.978
19:12273639:A:G	F254L	0.978

dbSNP variants (sampled 300 via entrez): RS1000001927 (19:12269818 G>A), RS1000043932 (19:12260917 A>G), RS1000050051 (19:12227951 T>G), RS1000083734 (19:12289414 AC>A), RS1000096087 (19:12290465 G>A,C), RS1000102420 (19:12248828 G>T), RS1000138828 (19:12255508 T>C,G), RS1000244836 (19:12293606 C>A,G), RS1000258469 (19:12252093 A>G), RS1000355408 (19:12251919 C>A,T), RS1000357381 (19:12230980 T>C), RS1000419738 (19:12257678 G>A), RS1000486042 (19:12227631 T>C), RS1000500936 (19:12295975 C>G), RS1000505568 (19:12269468 G>A)

Disease associations

OMIM: gene MIM:194542 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cadmium Chloride	increases expression, increases abundance	2
aristolochic acid I	increases expression	1
TAK-243	increases sumoylation	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
geraniol	increases expression	1
trichostatin A	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
hydroquinone	decreases expression	1
vanadyl sulfate	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
Resveratrol	affects cotreatment, increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Benzo(a)pyrene	increases methylation, affects methylation, decreases methylation	1
Cadmium	increases abundance, increases expression	1
Cisplatin	increases expression	1
Coal	decreases expression, increases abundance	1
Coumestrol	decreases expression	1
Lead	affects methylation	1
Methotrexate	decreases expression	1
Nickel	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Smoke	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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