ZSWIM3

Summary

ZSWIM3 (zinc finger SWIM-type containing 3, HGNC:16157) is a protein-coding gene on chromosome 20q13.12, encoding Zinc finger SWIM domain-containing protein 3 (Q96MP5).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 140831 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_080752

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16157
Approved symbol	ZSWIM3
Name	zinc finger SWIM-type containing 3
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	dJ337O18.7, PPP1R174
Ensembl gene	ENSG00000132801
Ensembl biotype	protein_coding
OMIM	620336
Entrez	140831

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000255152, ENST00000926005

RefSeq mRNA: 1 — MANE Select: NM_080752 NM_080752

CCDS: CCDS13381

Canonical transcript exons

ENST00000255152 — 2 exons

Exon	Start	End
ENSE00001920359	45876714	45879122
ENSE00003666233	45857614	45857980

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.3455 / max 56.2602, expressed in 1683 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184955	5.3455	1683

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	98.37	gold quality
secondary oocyte	CL:0000655	98.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.78	gold quality
adrenal tissue	UBERON:0018303	78.84	gold quality
kidney epithelium	UBERON:0004819	77.53	gold quality
granulocyte	CL:0000094	74.93	gold quality
upper arm skin	UBERON:0004263	74.71	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	74.60	gold quality
pancreatic ductal cell	CL:0002079	74.49	silver quality
mucosa of transverse colon	UBERON:0004991	74.39	gold quality
endothelial cell	CL:0000115	73.74	silver quality
nasal cavity epithelium	UBERON:0005384	73.21	gold quality
stromal cell of endometrium	CL:0002255	72.12	gold quality
right adrenal gland	UBERON:0001233	71.93	gold quality
right adrenal gland cortex	UBERON:0035827	71.88	gold quality
cortical plate	UBERON:0005343	71.38	gold quality
lateral nuclear group of thalamus	UBERON:0002736	71.17	silver quality
lymph node	UBERON:0000029	70.83	gold quality
middle temporal gyrus	UBERON:0002771	70.55	silver quality
gingival epithelium	UBERON:0001949	70.29	gold quality
adrenal gland	UBERON:0002369	70.24	gold quality
sperm	CL:0000019	70.16	gold quality
adrenal cortex	UBERON:0001235	70.12	gold quality
left adrenal gland	UBERON:0001234	70.01	gold quality
left adrenal gland cortex	UBERON:0035825	69.97	gold quality
prefrontal cortex	UBERON:0000451	69.79	gold quality
myocardium	UBERON:0002349	69.79	gold quality
vena cava	UBERON:0004087	69.67	gold quality
cardiac muscle of right atrium	UBERON:0003379	69.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

44 targeting ZSWIM3, 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-6870-5P	99.99	68.55	2115
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-7-5P	99.67	70.53	1809
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-1276	99.36	68.18	1642
HSA-MIR-3678-3P	99.31	67.10	1432
HSA-MIR-6780B-3P	99.13	67.18	622
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-4656	98.79	66.22	1306

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zswim3	ENSMUSG00000045822
rattus_norvegicus	Zswim3	ENSRNOG00000015525

Paralogs (1): ZSWIM1 (ENSG00000168612)

Protein

Protein identifiers

Zinc finger SWIM domain-containing protein 3 — Q96MP5 (reviewed: Q96MP5)

All UniProt accessions (1): Q96MP5

RefSeq proteins (1): NP_542790* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006564	Znf_PMZ	Domain
IPR007527	Znf_SWIM	Domain
IPR045563	ZSWIM1/3_C	Domain
IPR048324	ZSWIM1-3_RNaseH-like	Domain
IPR048325	ZSWIM3_N	Domain
IPR048326	ZSWIM1-3_helical	Domain
IPR052579	Zinc_finger_SWIM	Family

Pfam: PF04434, PF19286, PF21056, PF21599, PF21600

UniProt features (5 total): sequence variant 2, chain 1, zinc finger region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96MP5-F1	72.17	0.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 63 (showing top): TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TGACCTY_ERR1_Q2, GGGTGGRR_PAX4_03, COUP_01, HNF4_01, PPAR_DR1_Q2, PPARG_01, SANSOM_APC_TARGETS_REQUIRE_MYC, GEORGES_TARGETS_OF_MIR192_AND_MIR215, COUP_DR1_Q6, MZF1_01, VDR_Q6, CACBINDINGPROTEIN_Q6, PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

1058 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSWIM3	LYG1	Q8N1E2	506
ZSWIM3	ANKS4B	Q8N8V4	484
ZSWIM3	ZNF507	Q8TCN5	449
ZSWIM3	IFT70A	Q86WT1	447
ZSWIM3	SMAP1	Q8IYB5	447
ZSWIM3	EPM2AIP1	Q7L775	446
ZSWIM3	CATSPERE	Q5SY80	428
ZSWIM3	SHROOM4	Q9ULL8	404
ZSWIM3	RTF2	Q9BY42	401
ZSWIM3	PHYHIPL	Q96FC7	389
ZSWIM3	DDX27	Q96GQ7	382
ZSWIM3	CRACR2A	Q9BSW2	382
ZSWIM3	TSPYL5	Q86VY4	375
ZSWIM3	USP6NL	Q92738	373
ZSWIM3	HENMT1	Q5T8I9	372
ZSWIM3	NOL4L	Q96MY1	372

IntAct

11 interactions, top by confidence:

A	B	Type	Score
ZSWIM3	GMCL1	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	ZSWIM3	psi-mi:“MI:0915”(physical association)	0.560
GMCL1	ZSWIM3	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	ZSWIM3	psi-mi:“MI:0915”(physical association)	0.560
PPP1CA	ZSWIM3	psi-mi:“MI:0407”(direct interaction)	0.440
ZSWIM3	CCDC57	psi-mi:“MI:0915”(physical association)	0.000
ZSWIM3	TRAF2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): ZSWIM3 (Two-hybrid), CCDC57 (Two-hybrid), ZSWIM3 (Positive Genetic), ZSWIM3 (Affinity Capture-MS), ZSWIM3 (Affinity Capture-Western)

ESM2 similar proteins: A0JN76, A2A5N8, A4IFA3, A4IGY9, D2EAC2, D3ZWK4, E1C2V1, O15060, O60290, O70445, O75132, P86452, Q08C99, Q0IJ29, Q13075, Q3UPF5, Q5BIW4, Q5T5X7, Q5T7W0, Q5TKR9, Q6DJS0, Q6EKJ0, Q6NRM8, Q6PAL0, Q6YI93, Q7Z2W4, Q7ZWZ4, Q801P1, Q80WQ9, Q80YY7, Q86UP8, Q8BZ21, Q8C4P0, Q8CFL8, Q8N8K9, Q8NCP5, Q8WML3, Q92794, Q96MP5, Q96Q42

Diamond homologs: Q8CFL8, Q96MP5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	77
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

383 predictions. Top by Δscore:

Variant	Effect	Δscore
20:45857981:G:GG	donor_gain	1.0000
20:45857986:G:GT	donor_gain	1.0000
20:45857970:G:GT	donor_gain	0.9900
20:45857976:ATCCT:A	donor_gain	0.9900
20:45857977:TCCT:T	donor_gain	0.9900
20:45857979:CTG:C	donor_loss	0.9900
20:45857980:TG:T	donor_loss	0.9900
20:45857981:G:GA	donor_loss	0.9900
20:45857982:T:A	donor_loss	0.9900
20:45876709:CCTA:C	acceptor_loss	0.9900
20:45876713:GGTAT:G	acceptor_gain	0.9900
20:45857891:G:GT	donor_gain	0.9800
20:45857978:CCT:C	donor_gain	0.9800
20:45857979:CT:C	donor_gain	0.9800
20:45858898:GGAT:G	donor_gain	0.9800
20:45876712:AG:A	acceptor_gain	0.9800
20:45876713:GG:G	acceptor_gain	0.9800
20:45857918:GGAC:G	donor_gain	0.9700
20:45876713:GGT:G	acceptor_gain	0.9600
20:45870676:C:G	donor_gain	0.9500
20:45876711:TAGG:T	acceptor_gain	0.9500
20:45876713:GGTA:G	acceptor_gain	0.9500
20:45876709:CCTAG:C	acceptor_gain	0.9400
20:45876710:CTAGG:C	acceptor_gain	0.9400
20:45876712:A:T	acceptor_gain	0.9400
20:45876713:G:T	acceptor_gain	0.9400
20:45876712:A:AG	acceptor_gain	0.9300
20:45876713:G:GG	acceptor_gain	0.9300
20:45876708:CCCTA:C	acceptor_gain	0.9200
20:45857919:G:T	donor_gain	0.8900

AlphaMissense

4617 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:45877168:A:C	S204R	0.995
20:45877170:C:A	S204R	0.995
20:45877170:C:G	S204R	0.995
20:45877666:T:A	W370R	0.993
20:45877666:T:C	W370R	0.993
20:45877687:T:A	W377R	0.990
20:45877687:T:C	W377R	0.990
20:45876736:T:C	C60R	0.987
20:45877312:G:C	A252P	0.985
20:45877403:T:A	V282D	0.985
20:45877475:C:T	S306F	0.985
20:45877655:T:C	L366P	0.985
20:45877220:T:C	L221P	0.983
20:45878234:T:C	L559P	0.983
20:45876784:T:C	C76R	0.982
20:45878239:T:C	C561R	0.982
20:45877172:T:C	F205S	0.981
20:45877177:A:C	S207R	0.981
20:45877179:C:A	S207R	0.981
20:45877179:C:G	S207R	0.981
20:45877364:T:C	F269S	0.980
20:45877689:G:C	W377C	0.980
20:45877689:G:T	W377C	0.980
20:45877166:T:C	L203P	0.979
20:45877668:G:C	W370C	0.979
20:45877668:G:T	W370C	0.979
20:45857863:T:C	F13S	0.978
20:45877304:T:A	V249E	0.977
20:45876803:T:C	L82P	0.975
20:45877207:T:C	F217L	0.975

dbSNP variants (sampled 300 via entrez): RS1000015176 (20:45867433 T>C), RS1000196622 (20:45871499 C>T), RS1000312872 (20:45871148 A>C), RS1000530795 (20:45869962 G>A,T), RS1000645319 (20:45869669 C>T), RS1000675447 (20:45874096 T>C,G), RS1000736491 (20:45879469 G>A), RS1000832971 (20:45864847 T>A), RS1001002691 (20:45876610 G>T), RS1001096348 (20:45863834 C>A,T), RS1001432258 (20:45860863 G>A), RS1001519052 (20:45865632 G>C), RS1001569878 (20:45867730 G>A), RS1001570063 (20:45865832 C>A,T), RS1001600954 (20:45867508 G>T)

Disease associations

OMIM: gene MIM:620336 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Cadmium	increases abundance, increases expression, decreases expression	2
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
bisphenol A	affects cotreatment, increases expression	1
titanium dioxide	decreases expression	1
sodium arsenite	increases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	decreases expression	1
Vitamin K 3	affects expression	1

Clinical trials (associated diseases)

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