ZSWIM1

Summary

ZSWIM1 (zinc finger SWIM-type containing 1, HGNC:16155) is a protein-coding gene on chromosome 20q13.12, encoding Zinc finger SWIM domain-containing protein 1 (Q9BR11).

Predicted to enable zinc ion binding activity. Predicted to be located in nucleus.

Source: NCBI Gene 90204 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 66 total
• MANE Select transcript: NM_080603

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16155
Approved symbol	ZSWIM1
Name	zinc finger SWIM-type containing 1
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	dJ337O18.5
Ensembl gene	ENSG00000168612
Ensembl biotype	protein_coding
Entrez	90204

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000372523, ENST00000853422

RefSeq mRNA: 1 — MANE Select: NM_080603 NM_080603

CCDS: CCDS13382

Canonical transcript exons

ENST00000372523 — 2 exons

Exon	Start	End
ENSE00001458013	45882533	45885266
ENSE00001458014	45881227	45881261

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 87.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3104 / max 117.9609, expressed in 1755 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
184957	6.8602	1747
184956	0.4502	201

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	87.50	silver quality
tibialis anterior	UBERON:0001385	86.64	silver quality
ileal mucosa	UBERON:0000331	86.45	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.50	gold quality
nasal cavity epithelium	UBERON:0005384	83.29	gold quality
kidney epithelium	UBERON:0004819	82.03	gold quality
hindlimb stylopod muscle	UBERON:0004252	80.91	gold quality
right adrenal gland	UBERON:0001233	80.59	gold quality
muscle of leg	UBERON:0001383	80.41	gold quality
gastrocnemius	UBERON:0001388	80.33	gold quality
stromal cell of endometrium	CL:0002255	80.10	gold quality
right adrenal gland cortex	UBERON:0035827	80.02	gold quality
apex of heart	UBERON:0002098	79.73	gold quality
left adrenal gland	UBERON:0001234	79.72	gold quality
islet of Langerhans	UBERON:0000006	79.66	gold quality
left adrenal gland cortex	UBERON:0035825	79.15	gold quality
cerebellar hemisphere	UBERON:0002245	78.92	gold quality
cerebellar cortex	UBERON:0002129	78.87	gold quality
adrenal gland	UBERON:0002369	78.52	gold quality
mucosa of transverse colon	UBERON:0004991	78.34	gold quality
adrenal cortex	UBERON:0001235	78.31	gold quality
heart right ventricle	UBERON:0002080	78.29	gold quality
upper arm skin	UBERON:0004263	78.29	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.16	gold quality
adrenal tissue	UBERON:0018303	78.02	gold quality
cerebellum	UBERON:0002037	77.92	gold quality
deltoid	UBERON:0001476	77.88	silver quality
heart left ventricle	UBERON:0002084	77.78	gold quality
cardiac ventricle	UBERON:0002082	77.65	gold quality
left ovary	UBERON:0002119	77.54	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-4850	no	20.03
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting ZSWIM1, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-574-5P	100.00	66.01	989
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-6778-3P	99.96	67.29	2693
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-6745	99.74	65.33	1321
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-363-5P	99.46	64.51	1015
HSA-MIR-6165	99.44	67.12	1389
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-320A-5P	98.88	66.75	1248
HSA-MIR-4764-5P	98.88	65.53	894
HSA-MIR-330-5P	98.73	67.63	1788
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-326	98.25	66.44	1565
HSA-MIR-4768-3P	98.16	66.02	2330
HSA-MIR-4483	98.09	64.12	1642
HSA-MIR-122-5P	97.23	64.92	1024
HSA-MIR-610	96.84	67.98	905
HSA-MIR-2355-3P	96.84	68.54	909
HSA-MIR-6894-3P	96.73	65.64	798

Literature-anchored findings (GeneRIF, showing 3)

• The activation sensitive nature of ZSWIM1 expression suggests that it may play a novel role in the development or function of T helper cells. (PMID:24508175)
• ZSWIM1 Promotes the Proliferation and Metastasis of Lung Adenocarcinoma Cells through the STK38/MEKK2/ERK1/2 Axis. (PMID:36511424)
• [TRIM21 Inhibits the Proliferation and Migration of Lung Adenocarcinoma Cells by Interacting with ZSWIM1]. (PMID:38880921)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zswim1	ENSMUSG00000017764
rattus_norvegicus	Zswim1	ENSRNOG00000015735

Paralogs (1): ZSWIM3 (ENSG00000132801)

Protein

Protein identifiers

Zinc finger SWIM domain-containing protein 1 — Q9BR11 (reviewed: Q9BR11)

All UniProt accessions (1): Q9BR11

RefSeq proteins (1): NP_542170* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF04434, PF19286, PF21056, PF21600

UniProt features (3 total): chain 1, zinc finger region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BR11-F1	76.24	0.34

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 61 (showing top): TGACCTY_ERR1_Q2, RFX1_02, DELACROIX_RAR_BOUND_ES, RAO_BOUND_BY_SALL4_ISOFORM_B, PRC1_BMI_UP.V1_UP, DCA_UP.V1_UP, KRAS.PROSTATE_UP.V1_UP, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, GREB1_TARGET_GENES, PRKDC_TARGET_GENES, SKIL_TARGET_GENES, WIZ_TARGET_GENES, ZFHX3_TARGET_GENES, ZNF407_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), 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
transition metal ion binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

898 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSWIM1	ZSWIM9	Q86XI8	732
ZSWIM1	SPATA25	Q9BR10	628
ZSWIM1	WFDC10B	Q8IUB3	580
ZSWIM1	NEURL2	Q9BR09	541
ZSWIM1	SNX21	Q969T3	507
ZSWIM1	WFDC3	Q8IUB2	490
ZSWIM1	A0A0G2JP48	A0A0G2JP48	479
ZSWIM1	ZNF221	Q9UK13	478
ZSWIM1	ZNF335	Q9H4Z2	475
ZSWIM1	SYS1	Q8N2H4	431
ZSWIM1	OR10J1	P30954	419
ZSWIM1	OR11A1	Q9GZK7	419
ZSWIM1	TMEM215	Q68D42	413
ZSWIM1	ACOT8	O14734	400
ZSWIM1	TRIR	Q9BQ61	400

IntAct

5 interactions, top by confidence:

A	B	Type	Score
SCRIB	ZSWIM1	psi-mi:“MI:0915”(physical association)	0.400
	ZSWIM1	psi-mi:“MI:0915”(physical association)	0.000
ZSWIM1	yapC	psi-mi:“MI:0915”(physical association)	0.000
gabD	ZSWIM1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): ZSWIM1 (Affinity Capture-RNA), ZSWIM1 (Affinity Capture-RNA), ZSWIM1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A7H0DNF0, A1A5R7, B7F7B9, B9A014, F1MIW6, F4HZD1, F4JLK2, O14138, O14423, O23702, O60106, P0DSU9, P0DSV0, P24915, P34751, P36052, P38960, P49777, P52924, P70190, P86452, Q196W7, Q1L6Q1, Q4R7M8, Q5Q0E6, Q6IND4, Q6TEQ0, Q80HX3, Q80TC5, Q84RQ9, Q8CDS7, Q8CFL8, Q8L7T6, Q8QMP8, Q8V4S4, Q96KX2, Q9BR11, Q9DCE9, Q9FFN9, Q9FFP1

Diamond homologs: Q9BR11, Q9CWV7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	60
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

270 predictions. Top by Δscore:

Variant	Effect	Δscore
20:45882527:CCATA:C	acceptor_loss	0.9500
20:45882528:CATA:C	acceptor_loss	0.9500
20:45882529:ATAGG:A	acceptor_loss	0.9500
20:45882530:TAGGC:T	acceptor_loss	0.9500
20:45882531:A:AG	acceptor_gain	0.9500
20:45882531:AGGCC:A	acceptor_loss	0.9500
20:45882532:G:GG	acceptor_gain	0.9500
20:45881336:G:T	donor_gain	0.9300
20:45881345:G:T	donor_gain	0.9300
20:45881260:GG:G	donor_gain	0.9200
20:45881261:GG:G	donor_gain	0.9200
20:45881263:TGAGT:T	donor_loss	0.9200
20:45881264:GAGTG:G	donor_loss	0.9200
20:45881265:A:AC	donor_loss	0.9200
20:45881266:G:C	donor_loss	0.9200
20:45881532:TGGGC:T	donor_gain	0.9100
20:45882430:GAACA:G	acceptor_gain	0.9100
20:45882532:GGCCC:G	acceptor_gain	0.9100
20:45881262:G:GG	donor_gain	0.9000
20:45881533:GGGCA:G	donor_gain	0.8900
20:45881523:GA:G	donor_gain	0.8800
20:45881258:GTGG:G	donor_gain	0.8700
20:45881536:C:T	donor_gain	0.8500
20:45881528:A:AG	donor_gain	0.8300
20:45881514:C:G	donor_gain	0.8200
20:45881414:TAGAG:T	donor_loss	0.8000
20:45881415:AGAGG:A	donor_loss	0.8000
20:45881417:AGGT:A	donor_loss	0.8000
20:45881419:G:GA	donor_loss	0.8000
20:45881420:T:A	donor_loss	0.8000

AlphaMissense

3195 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:45883772:T:C	C394R	0.981
20:45883103:T:C	F171L	0.978
20:45883105:C:A	F171L	0.978
20:45883105:C:G	F171L	0.978
20:45883616:T:C	C342R	0.978
20:45883767:T:C	L392P	0.978
20:45883780:C:A	H396Q	0.978
20:45883780:C:G	H396Q	0.978
20:45882991:G:C	K133N	0.976
20:45882991:G:T	K133N	0.976
20:45883774:C:G	C394W	0.976
20:45884018:T:A	W476R	0.975
20:45884018:T:C	W476R	0.975
20:45883773:G:A	C394Y	0.974
20:45883073:T:C	F161L	0.970
20:45883074:T:C	F161S	0.970
20:45883075:C:A	F161L	0.970
20:45883075:C:G	F161L	0.970
20:45884001:G:C	R470P	0.970
20:45884007:T:C	L472P	0.970
20:45884010:C:A	A473D	0.969
20:45882927:T:A	V112D	0.968
20:45883310:T:A	W240R	0.966
20:45883310:T:C	W240R	0.966
20:45883742:T:C	C384R	0.965
20:45884009:G:C	A473P	0.965
20:45883581:T:A	L330H	0.964
20:45883736:T:C	C382R	0.964
20:45883772:T:A	C394S	0.962
20:45883773:G:C	C394S	0.962

dbSNP variants (sampled 300 via entrez): RS1000736491 (20:45879469 G>A), RS1001055911 (20:45883324 C>G), RS1001719583 (20:45881587 A>G), RS1002793135 (20:45880083 G>A), RS1003195188 (20:45881265 A>T), RS1003689066 (20:45885603 G>A,T), RS1005153589 (20:45881730 T>C), RS1005177097 (20:45879278 C>T), RS1005275272 (20:45885009 TA>T,TAA), RS1005807114 (20:45885687 G>A), RS1005822498 (20:45884679 A>C), RS1006031167 (20:45884082 C>G,T), RS1006625106 (20:45879191 A>T), RS1007029698 (20:45879688 G>C,T), RS1007412664 (20:45885165 A>G)

Disease associations

OMIM: gene `` | 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

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
dicrotophos	increases expression	1
butyraldehyde	decreases expression	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1
Urethane	decreases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Particulate Matter	affects cotreatment, decreases expression, increases abundance	1

Clinical trials (associated diseases)

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