ZFR2

Summary

ZFR2 (zinc finger RNA binding protein 2, HGNC:29189) is a protein-coding gene on chromosome 19p13.3, encoding Zinc finger RNA-binding protein 2 (Q9UPR6).

Predicted to enable double-stranded RNA binding activity and single-stranded RNA binding activity.

Source: NCBI Gene 23217 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 256 total
• MANE Select transcript: NM_015174

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29189
Approved symbol	ZFR2
Name	zinc finger RNA binding protein 2
Location	19p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000105278
Ensembl biotype	protein_coding
OMIM	619284
Entrez	23217

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000262961, ENST00000438164, ENST00000439086, ENST00000586578, ENST00000587212, ENST00000591712, ENST00000591965, ENST00000592398, ENST00000592807, ENST00000674260, ENST00000938272

RefSeq mRNA: 2 — MANE Select: NM_015174 NM_001145640, NM_015174

CCDS: CCDS45921, CCDS45922

Canonical transcript exons

ENST00000262961 — 19 exons

Exon	Start	End
ENSE00000664147	3831660	3831878
ENSE00000664149	3831303	3831556
ENSE00000664155	3827471	3827653
ENSE00000664167	3825230	3825407
ENSE00001597506	3804024	3806125
ENSE00001603270	3807172	3807269
ENSE00001609789	3821340	3821479
ENSE00001637716	3813820	3813958
ENSE00001653356	3810750	3810845
ENSE00001655567	3816674	3816845
ENSE00001785557	3808872	3808983
ENSE00001786015	3820182	3820290
ENSE00001791467	3811272	3811366
ENSE00001793228	3819045	3819235
ENSE00003535190	3823246	3823403
ENSE00003576352	3834773	3834983
ENSE00003611226	3833664	3833778
ENSE00003624304	3822081	3822200
ENSE00003845290	3868965	3869038

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 93.00.

FANTOM5 (CAGE): breadth broad, TPM avg 2.7146 / max 77.5798, expressed in 333 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
178341	2.6123	329
178342	0.1023	65

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pituitary gland	UBERON:0000007	93.00	gold quality
adenohypophysis	UBERON:0002196	92.73	gold quality
Brodmann (1909) area 23	UBERON:0013554	88.66	gold quality
middle temporal gyrus	UBERON:0002771	87.21	gold quality
right testis	UBERON:0004534	86.82	gold quality
left testis	UBERON:0004533	86.58	gold quality
right frontal lobe	UBERON:0002810	86.34	gold quality
primary visual cortex	UBERON:0002436	85.75	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.68	gold quality
cingulate cortex	UBERON:0003027	84.66	gold quality
anterior cingulate cortex	UBERON:0009835	84.56	gold quality
testis	UBERON:0000473	84.12	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.77	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.71	gold quality
nucleus accumbens	UBERON:0001882	83.39	gold quality
endothelial cell	CL:0000115	83.20	gold quality
cortical plate	UBERON:0005343	83.05	gold quality
pigmented layer of retina	UBERON:0001782	82.32	gold quality
retina	UBERON:0000966	82.30	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.90	gold quality
amygdala	UBERON:0001876	81.52	gold quality
hypothalamus	UBERON:0001898	81.19	gold quality
neocortex	UBERON:0001950	80.39	gold quality
forebrain	UBERON:0001890	80.31	gold quality
cerebral cortex	UBERON:0000956	80.19	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	79.60	gold quality
occipital lobe	UBERON:0002021	79.56	gold quality
sperm	CL:0000019	79.44	silver quality
telencephalon	UBERON:0001893	79.27	gold quality
adult organism	UBERON:0007023	79.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.72

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting ZFR2, 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-4673	100.00	66.64	1490
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4503	99.85	71.45	1869
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-186-3P	99.51	66.24	1685
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	zfr2	ENSDARG00000071683
mus_musculus	Zfr2	ENSMUSG00000034949
rattus_norvegicus	Zfr2	ENSRNOG00000020416
drosophila_melanogaster	loqs	FBGN0032515
drosophila_melanogaster	CG12493	FBGN0035571
drosophila_melanogaster	blanks	FBGN0035608
drosophila_melanogaster	Zn72D	FBGN0263603
caenorhabditis_elegans	zfr-1	WBGENE00022388

Paralogs (14): STAU2 (ENSG00000040341), ZFR (ENSG00000056097), ADAT1 (ENSG00000065457), STAU1 (ENSG00000124214), ILF3 (ENSG00000129351), TARBP2 (ENSG00000139546), ADAD2 (ENSG00000140955), ILF2 (ENSG00000143621), ADAR (ENSG00000160710), ADAD1 (ENSG00000164113), STRBP (ENSG00000165209), PRKRA (ENSG00000180228), ADARB2 (ENSG00000185736), ADARB1 (ENSG00000197381)

Protein

Protein identifiers

Zinc finger RNA-binding protein 2 — Q9UPR6 (reviewed: Q9UPR6)

All UniProt accessions (5): Q9UPR6, A0A6I8PRF6, K7EKD7, K7EPY6, K7EQC0

Isoforms (3)

UniProt ID	Names	Canonical?
Q9UPR6-1	1	yes
Q9UPR6-2	2
Q9UPR6-3	3

RefSeq proteins (2): NP_001139112, NP_055989* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003604	Matrin/U1-like-C_Znf_C2H2	Domain
IPR006561	DZF_dom	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR043519	NT_sf	Homologous_superfamily
IPR049401	DZF_dom_N	Domain
IPR049402	DZF_dom_C	Domain

Pfam: PF07528, PF12874, PF20965

UniProt features (27 total): region of interest 8, sequence variant 7, compositionally biased region 4, splice variant 4, chain 1, domain 1, coiled-coil region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UPR6-F1	64.88	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 106 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, TSENG_IRS1_TARGETS_DN, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, chr19p13, GOMF_SINGLE_STRANDED_RNA_BINDING, MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP, KOYAMA_SEMA3B_TARGETS_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, E2F1_UP.V1_DN, PGF_UP.V1_DN, ATF2_S_UP.V1_UP, ATF2_UP.V1_UP, SALL4_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (4): double-stranded RNA binding (GO:0003725), single-stranded RNA binding (GO:0003727), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA binding	2
transition metal ion binding	1
binding	1

Protein interactions and networks

STRING

502 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZFR2	RBM7	Q9Y580	446
ZFR2	FUS	P35637	426
ZFR2	ZNF169	Q14929	402
ZFR2	NANOS2	P60321	401
ZFR2	ZFP36L1	Q07352	397
ZFR2	ZFR	Q96KR1	384
ZFR2	ENTPD6	O75354	370
ZFR2	PDGFC	Q9NRA1	358
ZFR2	PTPN14	Q15678	355
ZFR2	ENG	P17813	338
ZFR2	VEGFB	P49765	334
ZFR2	ZFP36	P26651	330
ZFR2	SPATC1	Q76KD6	329
ZFR2	NMRK2	Q9NPI5	329
ZFR2	FAM169A	Q9Y6X4	325

IntAct

1 interactions, top by confidence:

A	B	Type	Score
	AP3B1	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): ILF2 (Co-fractionation), ZFR2 (Co-fractionation), ZFR2 (Affinity Capture-MS), ZFR2 (Protein-RNA), ZFR2 (Affinity Capture-MS)

ESM2 similar proteins: A0JPN4, A1YF56, A2A288, A2A9T0, A2AEV7, A6QQJ8, A7MCY6, A8MVW0, D3ZG83, D3ZZN9, O09039, O15037, O75427, O94983, O95382, O95947, P0C5W1, P98077, Q02779, Q16584, Q2M3V2, Q53LP3, Q5D1E7, Q5D1E8, Q66HA1, Q66K74, Q66L42, Q6DG50, Q6ZUM4, Q6ZW31, Q76KP1, Q7T0L4, Q7TSG2, Q80XI6, Q80Y50, Q8BIY3, Q8BLS7, Q8K120, Q8K1S6, Q8R5G7

Diamond homologs: O88532, Q08E27, Q0VD35, Q12906, Q562A2, Q5R6Y5, Q5REX3, Q5U231, Q5ZIL4, Q6DCD0, Q6DD04, Q6GL57, Q6GPM1, Q6NXA4, Q6PCR6, Q7TP98, Q91550, Q91WM1, Q96KR1, Q96SI9, Q9H898, Q9JIL3, Q9JKU6, Q9UPR6, Q9Z1X4, B8GAM6, P51400, P78563, P97616, Q12905, Q5RFJ1, Q6NZ06, Q6P8G1, Q7ZW47, Q8CJ67, Q91ZS8, Q9CXY6, Q9JI20, Q9NII1, Q9NS39

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	219
Likely benign	26
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4303 predictions. Top by Δscore:

Variant	Effect	Δscore
19:3807292:A:T	acceptor_gain	1.0000
19:3810744:CCTTA:C	donor_loss	1.0000
19:3810745:CTTA:C	donor_loss	1.0000
19:3810746:TTACC:T	donor_loss	1.0000
19:3810747:TACCC:T	donor_loss	1.0000
19:3810748:A:AT	donor_loss	1.0000
19:3813814:CCGCA:C	donor_loss	1.0000
19:3813815:CGCA:C	donor_loss	1.0000
19:3813816:GCACC:G	donor_loss	1.0000
19:3813817:CACCT:C	donor_loss	1.0000
19:3813818:A:AT	donor_loss	1.0000
19:3813819:C:CA	donor_loss	1.0000
19:3813955:CCAT:C	acceptor_gain	1.0000
19:3813956:CATC:C	acceptor_gain	1.0000
19:3813957:ATCT:A	acceptor_loss	1.0000
19:3816670:TTAC:T	donor_loss	1.0000
19:3816672:A:AC	donor_gain	1.0000
19:3816673:C:CC	donor_gain	1.0000
19:3816841:CGCTG:C	acceptor_gain	1.0000
19:3816843:CTG:C	acceptor_gain	1.0000
19:3816844:TG:T	acceptor_gain	1.0000
19:3818899:T:TA	donor_gain	1.0000
19:3819063:T:TA	donor_gain	1.0000
19:3819231:CCGGG:C	acceptor_gain	1.0000
19:3819232:CGGG:C	acceptor_gain	1.0000
19:3819232:CGGGC:C	acceptor_gain	1.0000
19:3819236:C:CC	acceptor_gain	1.0000
19:3820178:CTA:C	donor_loss	1.0000
19:3820179:TA:T	donor_loss	1.0000
19:3820180:A:C	donor_loss	1.0000

AlphaMissense

6010 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:3806102:G:C	F889L	0.998
19:3806102:G:T	F889L	0.998
19:3806104:A:G	F889L	0.998
19:3822098:G:C	H492D	0.997
19:3822154:C:G	C473S	0.997
19:3822154:C:T	C473Y	0.997
19:3822155:A:T	C473S	0.997
19:3822163:C:T	C470Y	0.997
19:3827639:A:C	H289Q	0.997
19:3827639:A:T	H289Q	0.997
19:3822086:A:C	Y496D	0.996
19:3822162:G:C	C470W	0.996
19:3822163:C:G	C470S	0.996
19:3822164:A:T	C470S	0.996
19:3822168:G:C	F468L	0.996
19:3822168:G:T	F468L	0.996
19:3822170:A:G	F468L	0.996
19:3831328:C:G	C276S	0.996
19:3831328:C:T	C276Y	0.996
19:3831329:A:T	C276S	0.996
19:3822098:G:T	H492N	0.995
19:3822116:G:C	H486D	0.995
19:3822154:C:A	C473F	0.995
19:3822155:A:G	C473R	0.995
19:3822163:C:A	C470F	0.995
19:3827535:C:G	C324S	0.995
19:3827536:A:T	C324S	0.995
19:3827623:G:C	H295D	0.995
19:3827641:G:C	H289D	0.995
19:3827641:G:T	H289N	0.995

dbSNP variants (sampled 300 via entrez): RS1000021375 (19:3853847 T>C), RS1000135816 (19:3838088 C>A,T), RS1000170926 (19:3819432 A>C), RS1000280143 (19:3814687 G>A,C), RS1000341076 (19:3846548 C>T), RS1000474065 (19:3839077 G>A), RS1000593288 (19:3804265 G>A), RS1000626269 (19:3819706 G>A), RS1000713917 (19:3838864 G>A), RS1000733248 (19:3824363 A>T), RS1000795746 (19:3846802 C>T), RS1000832838 (19:3807571 G>A), RS1000873130 (19:3859716 A>G), RS1000885478 (19:3842629 T>G), RS1000930271 (19:3808425 G>A,T)

Disease associations

OMIM: gene MIM:619284 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST007637_40	Diffusing capacity of carbon monoxide	6.000000e-06
GCST008129_61	Body mass index	2.000000e-07
GCST008513_34	Health literacy	4.000000e-06
GCST012489_82	Heel bone mineral density x serum urate levels interaction	6.000000e-09

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0009369	diffusing capacity of the lung for carbon monoxide
EFO:0004340	body mass index
EFO:0010104	health literacy measurement
EFO:0004531	urate measurement
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases methylation, increases expression	2
Benzo(a)pyrene	affects methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	increases methylation, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
aflatoxin B2	decreases methylation	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	increases methylation	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects methylation	1
Carbamazepine	affects expression	1
Estradiol	increases expression	1
Phthalic Acids	increases methylation	1
Rotenone	increases expression	1
Tretinoin	decreases expression	1
Aflatoxin B1	affects methylation	1
Cadmium Chloride	increases expression	1

Clinical trials (associated diseases)

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