ZFP37

Summary

ZFP37 (ZFP37 zinc finger protein, HGNC:12863) is a protein-coding gene on chromosome 9q32, encoding Zinc finger protein 37 homolog (Q9Y6Q3). May be involved in transcriptional regulation.

This gene encodes a transcription factor that belongs to a large family of zinc finger proteins. A similar protein in mouse is thought to play a role in regulating the structures of the nucleolus and centromere in neurons. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 7539 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 81 total
• MANE Select transcript: NM_003408

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12863
Approved symbol	ZFP37
Name	ZFP37 zinc finger protein
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	ZNF906
Ensembl gene	ENSG00000136866
Ensembl biotype	protein_coding
OMIM	602951
Entrez	7539

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000374227, ENST00000553380, ENST00000555206, ENST00000940564, ENST00000948256

RefSeq mRNA: 3 — MANE Select: NM_003408 NM_001282515, NM_001282518, NM_003408

CCDS: CCDS65109, CCDS65110, CCDS6787

Canonical transcript exons

ENST00000374227 — 4 exons

Exon	Start	End
ENSE00000806242	113049362	113049496
ENSE00001317422	113049791	113049872
ENSE00001462839	113038377	113044268
ENSE00001462841	113056557	113056724

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 84.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.9401 / max 108.5483, expressed in 1151 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102078	3.6594	1109
102079	0.2807	133

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	84.93	gold quality
ganglionic eminence	UBERON:0004023	81.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.83	gold quality
ventricular zone	UBERON:0003053	78.58	gold quality
calcaneal tendon	UBERON:0003701	76.86	gold quality
islet of Langerhans	UBERON:0000006	75.23	gold quality
embryo	UBERON:0000922	73.35	gold quality
stromal cell of endometrium	CL:0002255	73.06	gold quality
left ovary	UBERON:0002119	72.50	gold quality
right ovary	UBERON:0002118	72.29	gold quality
cerebellar hemisphere	UBERON:0002245	71.59	gold quality
cerebellar cortex	UBERON:0002129	71.55	gold quality
ovary	UBERON:0000992	71.36	gold quality
right hemisphere of cerebellum	UBERON:0014890	71.21	gold quality
body of uterus	UBERON:0009853	70.33	gold quality
cerebellum	UBERON:0002037	70.28	gold quality
descending thoracic aorta	UBERON:0002345	69.82	gold quality
right coronary artery	UBERON:0001625	68.56	gold quality
mucosa of stomach	UBERON:0001199	68.45	gold quality
endocervix	UBERON:0000458	68.44	gold quality
smooth muscle tissue	UBERON:0001135	68.17	gold quality
pituitary gland	UBERON:0000007	67.99	gold quality
left coronary artery	UBERON:0001626	67.66	gold quality
adenohypophysis	UBERON:0002196	67.64	gold quality
pigmented layer of retina	UBERON:0001782	67.57	gold quality
popliteal artery	UBERON:0002250	67.56	gold quality
tibial artery	UBERON:0007610	67.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	67.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.52	gold quality
prefrontal cortex	UBERON:0000451	67.48	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.59

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

48 targeting ZFP37, 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-6833-3P	100.00	70.63	3197
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-9-3P	99.96	70.88	2068
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-5689	99.50	71.26	1154
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-4666A-5P	99.41	69.72	1887

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zfp37	ENSMUSG00000028389
rattus_norvegicus	Zfp37-ps1	ENSRNOG00000046629
rattus_norvegicus	AABR07048473.1	ENSRNOG00000051164
rattus_norvegicus	Zfp37	ENSRNOG00000069865
drosophila_melanogaster	CG2712	FBGN0024975
drosophila_melanogaster	Phs	FBGN0036522
drosophila_melanogaster	CG3281	FBGN0260741

Paralogs (62): ZNF582 (ENSG00000018869), ZNF264 (ENSG00000083844), ZNF343 (ENSG00000088876), ZNF684 (ENSG00000117010), ZNF133 (ENSG00000125846), ZNF557 (ENSG00000130544), ZNF337 (ENSG00000130684), ZNF20 (ENSG00000132010), ZNF614 (ENSG00000142556), KRBOX4 (ENSG00000147121), ZNF599 (ENSG00000153896), ZNF19 (ENSG00000157429), ZNF589 (ENSG00000164048), PRDM9 (ENSG00000164256), ZNF180 (ENSG00000167384), ZNF558 (ENSG00000167785), ZNF35 (ENSG00000169981), ZNF778 (ENSG00000170100), ZNF439 (ENSG00000171291), ZNF440 (ENSG00000171295), ZNF556 (ENSG00000172000), ZNF554 (ENSG00000172006), ZNF596 (ENSG00000172748), ZNF80 (ENSG00000174255), ZNF266 (ENSG00000174652), ZNF25 (ENSG00000175395), ZNF77 (ENSG00000175691), ZNF169 (ENSG00000175787), ZNF404 (ENSG00000176222), ZNF491 (ENSG00000177599), ZNF620 (ENSG00000177842), ZNF619 (ENSG00000177873), ZNF875 (ENSG00000181666), ZNF329 (ENSG00000181894), ZFP90 (ENSG00000184939), ZNF566 (ENSG00000186017), ZNF529 (ENSG00000186020), ZNF749 (ENSG00000186230), ZNF555 (ENSG00000186300), ZNF70 (ENSG00000187792)

Protein

Protein identifiers

Zinc finger protein 37 homolog — Q9Y6Q3 (reviewed: Q9Y6Q3)

All UniProt accessions (1): Q9Y6Q3

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Tissue specificity. Expressed at low level in several tissues including fetal cartilage.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y6Q3-1	1	yes
Q9Y6Q3-2	2
Q9Y6Q3-3	3

RefSeq proteins (3): NP_001269444, NP_001269447, NP_003399* (*=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
IPR056436	Znf-C2H2_ZIC1-5/GLI1-3-like	Domain

Pfam: PF00096, PF01352, PF23561

UniProt features (32 total): zinc finger region 12, compositionally biased region 7, sequence conflict 4, region of interest 3, splice variant 2, chain 1, domain 1, modified residue 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6Q3-F1	67.54	0.45

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): 42

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 80 (showing top): GGGNRMNNYCAT_UNKNOWN, YY1_Q6, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, MARTINEZ_RB1_TARGETS_DN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2, YY1_02, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GCCATNTTG_YY1_Q6, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, RAO_BOUND_BY_SALL4_ISOFORM_B, RELA_DN.V1_UP, NOTCH_DN.V1_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, E2F5_TARGET_GENES

GO Biological Process (3): regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892)

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), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), DNA binding (GO:0003677), 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	3
DNA-templated transcription	2
transcription cis-regulatory region binding	2
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription by RNA polymerase II	1
negative regulation of RNA biosynthetic process	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription regulator activity	1
transition metal ion binding	1
nucleic acid binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

472 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFP37	ZPR1	O75312	736
ZFP37	FHIT	P49789	661
ZFP37	SLC46A2	Q9BY10	617
ZFP37	SF3B4	Q15427	548
ZFP37	LMO2	P25791	478
ZFP37	SLC31A2	O15432	478
ZFP37	TAF11	Q15544	461
ZFP37	TAF9B	Q9HBM6	459
ZFP37	PBX1	P40424	447
ZFP37	PCDH17	O14917	427
ZFP37	C4orf33	Q8N1A6	418
ZFP37	BASP1	P80723	410
ZFP37	RUNX1T1	Q06455	397
ZFP37	CDH18	Q13634	387
ZFP37	MAGEA11	P43364	369

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ZFP37	CANX	psi-mi:“MI:0915”(physical association)	0.400
ZFP37	ECE1	psi-mi:“MI:0915”(physical association)	0.370
WDR46	NKRF	psi-mi:“MI:0914”(association)	0.350

BioGRID (6): ZFP37 (Affinity Capture-MS), ZFP37 (Affinity Capture-MS), ZFP37 (Proximity Label-MS), ZFP37 (Affinity Capture-MS), ZFP37 (Affinity Capture-MS), ZFP37 (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: A6NFI3, A6NM28, A6NNF4, A6QLU5, A8MQ14, A8MUV8, B4DU55, B4DX44, E9Q8G5, O60290, O75290, O75467, O94892, O95780, P0DPD5, P17014, P17031, P17032, P17097, P17098, P21506, P51523, P59923, Q02525, Q03936, Q05481, Q06732, Q08DG8, Q14586, Q14590, Q15928, Q16587, Q2M218, Q2TL60, Q3B7M4, Q3KQV3, Q3SXZ3, Q49AA0, Q4R6C2, Q4R8H9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	70
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

650 predictions. Top by Δscore:

Variant	Effect	Δscore
9:113049363:T:TA	donor_gain	1.0000
9:113056555:A:AC	donor_gain	1.0000
9:113056556:C:CC	donor_gain	1.0000
9:113049360:A:AC	donor_gain	0.9900
9:113049360:ACTT:A	donor_gain	0.9900
9:113049361:C:CC	donor_gain	0.9900
9:113049361:CTT:C	donor_gain	0.9900
9:113049361:CTTC:C	donor_gain	0.9900
9:113049493:CACC:C	acceptor_gain	0.9900
9:113049495:CC:C	acceptor_gain	0.9900
9:113049496:CC:C	acceptor_gain	0.9900
9:113056534:C:CA	donor_gain	0.9900
9:113056547:CAG:C	donor_gain	0.9900
9:113056552:CTCAC:C	donor_loss	0.9900
9:113056554:C:CG	donor_loss	0.9900
9:113056555:ACC:A	donor_loss	0.9900
9:113056556:CCG:C	donor_gain	0.9900
9:113056556:CCGC:C	donor_loss	0.9900
9:113044266:CTT:C	acceptor_gain	0.9800
9:113049354:CAACT:C	donor_loss	0.9800
9:113049355:AACTT:A	donor_loss	0.9800
9:113049356:ACTTA:A	donor_loss	0.9800
9:113049357:CTTAC:C	donor_loss	0.9800
9:113049358:T:TA	donor_loss	0.9800
9:113049359:T:TC	donor_loss	0.9800
9:113049360:A:C	donor_loss	0.9800
9:113049361:C:CT	donor_loss	0.9800
9:113049361:CT:C	donor_gain	0.9800
9:113049364:C:A	donor_gain	0.9800
9:113049497:C:CC	acceptor_gain	0.9800

AlphaMissense

4214 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:113042872:A:C	F582L	0.999
9:113042872:A:T	F582L	0.999
9:113042874:A:G	F582L	0.999
9:113042956:A:C	F554L	0.999
9:113042956:A:T	F554L	0.999
9:113042958:A:G	F554L	0.999
9:113043124:A:C	F498L	0.999
9:113043124:A:T	F498L	0.999
9:113043126:A:G	F498L	0.999
9:113042788:G:C	F610L	0.998
9:113042788:G:T	F610L	0.998
9:113042790:A:G	F610L	0.998
9:113042840:C:G	R593P	0.998
9:113042939:A:G	L560P	0.998
9:113043208:G:C	F470L	0.998
9:113043208:G:T	F470L	0.998
9:113043210:A:G	F470L	0.998
9:113043376:A:C	F414L	0.998
9:113043376:A:T	F414L	0.998
9:113043378:A:G	F414L	0.998
9:113043460:G:C	F386L	0.998
9:113043460:G:T	F386L	0.998
9:113043462:A:G	F386L	0.998
9:113043628:A:C	F330L	0.998
9:113043628:A:T	F330L	0.998
9:113043630:A:G	F330L	0.998
9:113042843:T:G	Q592P	0.997
9:113042855:A:G	L588P	0.997
9:113043040:A:C	F526L	0.997
9:113043040:A:T	F526L	0.997

dbSNP variants (sampled 300 via entrez): RS1000003441 (9:113038210 A>G), RS1000046363 (9:113045320 A>T), RS1000062362 (9:113038415 C>T), RS1000109458 (9:113055097 G>A), RS1000124039 (9:113039998 T>A,C), RS1000313089 (9:113045382 T>A,C), RS1000326493 (9:113052505 A>G,T), RS1000366088 (9:113038729 G>A), RS1000439671 (9:113038064 A>C), RS1000473270 (9:113058539 T>C,G), RS1000782545 (9:113051768 A>G), RS1000808301 (9:113057824 C>T), RS1000866453 (9:113058507 T>C), RS1001062516 (9:113050929 G>A), RS1001200619 (9:113037884 G>C)

Disease associations

OMIM: gene MIM:602951 | 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
GCST002931_15	Aluminium levels	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	4
sodium arsenite	decreases expression, increases abundance, increases expression	3
trichostatin A	affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
urushiol	decreases expression	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, decreases methylation	1
beta-lapachone	decreases expression, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	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, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
(+)-JQ1 compound	decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Acetaldehyde	increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cisplatin	decreases expression	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	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_XV96	HEK293 eGFP-ZFP37	Transformed cell line	Female

Clinical trials (associated diseases)

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