ZSWIM5

Summary

ZSWIM5 (zinc finger SWIM-type containing 5, HGNC:29299) is a protein-coding gene on chromosome 1p34.1, encoding Zinc finger SWIM domain-containing protein 5 (Q9P217).

Predicted to enable zinc ion binding activity. Located in extracellular space.

Source: NCBI Gene 57643 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 166 total
• MANE Select transcript: NM_020883

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29299
Approved symbol	ZSWIM5
Name	zinc finger SWIM-type containing 5
Location	1p34.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA1511
Ensembl gene	ENSG00000162415
Ensembl biotype	protein_coding
OMIM	620132
Entrez	57643

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000359600, ENST00000464588, ENST00000937275, ENST00000968055, ENST00000968056, ENST00000968057

RefSeq mRNA: 1 — MANE Select: NM_020883 NM_020883

CCDS: CCDS41319

Canonical transcript exons

ENST00000359600 — 14 exons

Exon	Start	End
ENSE00001064950	45034312	45034469
ENSE00001064952	45043219	45043395
ENSE00001064953	45035688	45035823
ENSE00001064954	45087881	45088237
ENSE00001064957	45038936	45039073
ENSE00001064958	45051074	45051253
ENSE00001064959	45040392	45040538
ENSE00001064960	45060099	45060247
ENSE00001064961	45020066	45020147
ENSE00001064962	45020625	45020788
ENSE00001064963	45036039	45036299
ENSE00001064964	45058609	45058759
ENSE00001412591	45205756	45206605
ENSE00001456967	45016399	45019316

Expression profiles

Bgee: expression breadth ubiquitous, 171 present calls, max score 92.02.

FANTOM5 (CAGE): breadth broad, TPM avg 2.6888 / max 61.0996, expressed in 798 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12108	1.2278	606
12107	1.1519	498
12109	0.3091	179

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	92.02	gold quality
pancreatic ductal cell	CL:0002079	85.20	silver quality
cortical plate	UBERON:0005343	85.08	gold quality
right adrenal gland	UBERON:0001233	84.41	gold quality
right adrenal gland cortex	UBERON:0035827	84.39	gold quality
left adrenal gland	UBERON:0001234	82.68	gold quality
ganglionic eminence	UBERON:0004023	82.37	gold quality
left adrenal gland cortex	UBERON:0035825	81.94	gold quality
adrenal cortex	UBERON:0001235	81.45	gold quality
adrenal gland	UBERON:0002369	81.15	gold quality
tibialis anterior	UBERON:0001385	81.06	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.77	gold quality
ventricular zone	UBERON:0003053	76.30	gold quality
left ovary	UBERON:0002119	76.14	gold quality
cerebellar cortex	UBERON:0002129	76.08	gold quality
cerebellar hemisphere	UBERON:0002245	76.06	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.91	gold quality
islet of Langerhans	UBERON:0000006	75.79	gold quality
right ovary	UBERON:0002118	75.79	gold quality
endothelial cell	CL:0000115	75.69	silver quality
cerebellum	UBERON:0002037	75.42	gold quality
adrenal tissue	UBERON:0018303	75.16	gold quality
rectum	UBERON:0001052	74.31	gold quality
mucosa of transverse colon	UBERON:0004991	74.06	gold quality
ovary	UBERON:0000992	73.87	gold quality
oviduct epithelium	UBERON:0004804	73.39	silver quality
pituitary gland	UBERON:0000007	73.04	gold quality
transverse colon	UBERON:0001157	72.90	gold quality
smooth muscle tissue	UBERON:0001135	72.07	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7008	yes	65.61
E-ANND-3	no	4.23

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

151 targeting ZSWIM5, 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-8485	100.00	77.57	4731
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4534	99.99	66.58	1907
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-507	99.97	70.11	1915
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	zswim5	ENSDARG00000055900
mus_musculus	Zswim5	ENSMUSG00000033948
rattus_norvegicus	Zswim5	ENSRNOG00000018160

Paralogs (3): ZSWIM6 (ENSG00000130449), ZSWIM4 (ENSG00000132003), ZSWIM8 (ENSG00000214655)

Protein

Protein identifiers

Zinc finger SWIM domain-containing protein 5 — Q9P217 (reviewed: Q9P217)

All UniProt accessions (1): Q9P217

RefSeq proteins (1): NP_065934* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007527	Znf_SWIM	Domain
IPR048370	ZSWIM4-8_C	Domain

Pfam: PF21055

UniProt features (6 total): region of interest 2, chain 1, zinc finger region 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P217-F1	81.89	0.59

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 78 (showing top): chr1p34, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, GOCC_TRANSFERASE_COMPLEX, GOCC_CULLIN_RING_UBIQUITIN_LIGASE_COMPLEX, GOCC_UBIQUITIN_LIGASE_COMPLEX, DODD_NASOPHARYNGEAL_CARCINOMA_DN, KRIEG_HYPOXIA_NOT_VIA_KDM3A, GOCC_CUL2_RING_UBIQUITIN_LIGASE_COMPLEX, ZBTB12_TARGET_GENES, ZNF597_TARGET_GENES, MIR8485, MIR340_5P, MIR12123, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, MIR5680

GO Biological Process (0):

GO Molecular Function (2): zinc ion binding (GO:0008270), metal ion binding (GO:0046872)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), Cul2-RING ubiquitin ligase complex (GO:0031462)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
cation binding	1
cullin-RING ubiquitin ligase complex	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSWIM5	PLEKHD1	A6NEE1	526
ZSWIM5	ZSWIM9	Q86XI8	497
ZSWIM5	KLHDC10	Q6PID8	399
ZSWIM5	C11orf52	Q96A22	391
ZSWIM5	ZNF766	Q5HY98	391
ZSWIM5	LRRC3B	Q96PB8	359
ZSWIM5	ABHD8	Q96I13	349
ZSWIM5	ZSCAN22	P10073	348
ZSWIM5	ZSWIM2	Q8NEG5	345
ZSWIM5	SOWAHA	Q2M3V2	335
ZSWIM5	ZNF404	Q494X3	323
ZSWIM5	FLACC1	Q96Q35	322
ZSWIM5	TAF4B	Q92750	311
ZSWIM5	SPATA18	Q8TC71	306
ZSWIM5	POU2AF2	Q8IXP5	306

IntAct

0 interactions, top by confidence:

BioGRID (8): ZSWIM5 (Affinity Capture-MS), ZSWIM5 (Affinity Capture-MS), ZSWIM5 (Affinity Capture-MS), ZSWIM5 (Affinity Capture-MS), ZSWIM5 (Affinity Capture-RNA), ZSWIM5 (Cross-Linking-MS (XL-MS)), GOLGB1 (Cross-Linking-MS (XL-MS)), ZSWIM5 (Affinity Capture-RNA)

ESM2 similar proteins: A0A571BF63, A0A8M9QN10, A1A4J7, A2AIV2, A2BID5, A2RRP1, A4D1P6, B0W730, B2RYI0, B3MJV4, B4GH42, B4MV81, B4Q9T2, B5E0H4, D4A039, O00750, O75153, P69735, Q0KK59, Q0VA04, Q0VDN7, Q17G65, Q1LXR6, Q2HJE1, Q3UHQ6, Q58D79, Q5JWR5, Q5PQS3, Q5R6T6, Q5SW19, Q5TYW4, Q5ZIB8, Q69YN4, Q6NUV0, Q6P4K6, Q6ZUJ8, Q7TMQ7, Q7Z3E5, Q80UJ7, Q8BL99

Diamond homologs: A7E2V4, A7E305, Q3UHH1, Q80TC6, Q8C7B8, Q9H7M6, Q9P217, Q9VWN9, Q80TB7, Q9HCJ5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	149
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3142 predictions. Top by Δscore:

Variant	Effect	Δscore
1:45040543:CAAG:C	acceptor_gain	1.0000
1:45043266:T:A	donor_gain	1.0000
1:45051070:TCACC:T	donor_loss	1.0000
1:45051071:CACC:C	donor_loss	1.0000
1:45051250:GCCC:G	acceptor_gain	1.0000
1:45051251:CCC:C	acceptor_gain	1.0000
1:45051251:CCCC:C	acceptor_gain	1.0000
1:45051252:CC:C	acceptor_gain	1.0000
1:45051252:CCC:C	acceptor_gain	1.0000
1:45051253:CC:C	acceptor_gain	1.0000
1:45051253:CCTG:C	acceptor_loss	1.0000
1:45051254:C:CC	acceptor_gain	1.0000
1:45051255:T:G	acceptor_loss	1.0000
1:45058604:CTTA:C	donor_loss	1.0000
1:45058605:TTA:T	donor_loss	1.0000
1:45058606:TA:T	donor_loss	1.0000
1:45058607:A:AT	donor_loss	1.0000
1:45058608:CCTAG:C	donor_gain	1.0000
1:45060095:TTACC:T	donor_loss	1.0000
1:45060096:TACC:T	donor_loss	1.0000
1:45060097:A:AC	donor_gain	1.0000
1:45060097:ACCT:A	donor_loss	1.0000
1:45060098:C:CC	donor_gain	1.0000
1:45060098:C:CG	donor_loss	1.0000
1:45060245:CAC:C	acceptor_gain	1.0000
1:45060248:C:CC	acceptor_gain	1.0000
1:45060248:CT:C	acceptor_loss	1.0000
1:45190555:TC:T	donor_gain	1.0000
1:45020626:TGTA:T	donor_gain	0.9900
1:45036034:CTTA:C	donor_loss	0.9900

AlphaMissense

7657 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:45018460:A:C	F1184L	1.000
1:45018460:A:T	F1184L	1.000
1:45018462:A:G	F1184L	1.000
1:45018485:A:C	L1176W	1.000
1:45018485:A:G	L1176S	1.000
1:45018490:T:A	K1174N	1.000
1:45018490:T:G	K1174N	1.000
1:45018491:T:A	K1174I	1.000
1:45018493:C:A	K1173N	1.000
1:45018493:C:G	K1173N	1.000
1:45018494:T:A	K1173M	1.000
1:45018494:T:G	K1173T	1.000
1:45018495:T:C	K1173E	1.000
1:45018498:C:A	G1172C	1.000
1:45018498:C:G	G1172R	1.000
1:45018499:T:A	K1171N	1.000
1:45018499:T:G	K1171N	1.000
1:45018504:A:C	Y1170D	1.000
1:45018515:A:G	L1166P	1.000
1:45018515:A:T	L1166H	1.000
1:45018527:A:G	F1162S	1.000
1:45018535:A:C	F1159L	1.000
1:45018535:A:T	F1159L	1.000
1:45018536:A:C	F1159C	1.000
1:45018536:A:G	F1159S	1.000
1:45018537:A:G	F1159L	1.000
1:45018578:G:T	A1145D	1.000
1:45018579:C:G	A1145P	1.000
1:45018587:A:G	L1142P	1.000
1:45018587:A:T	L1142Q	1.000

dbSNP variants (sampled 300 via entrez): RS1000002089 (1:45096722 T>C), RS1000021270 (1:45099867 T>C), RS1000031836 (1:45150663 A>G), RS1000035603 (1:45114269 T>C), RS1000043954 (1:45187544 G>C), RS1000060851 (1:45204123 A>G,T), RS1000090318 (1:45039192 C>G,T), RS1000100514 (1:45183054 G>A,C), RS1000158165 (1:45177783 C>T), RS1000163733 (1:45022574 T>C), RS1000169759 (1:45152473 T>C), RS1000210642 (1:45141098 A>G), RS1000250558 (1:45162192 AAAG>A), RS1000251192 (1:45202204 CCA>C), RS1000254310 (1:45070201 A>G)

Disease associations

OMIM: gene MIM:620132 | 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
GCST012227_1398	Hip circumference adjusted for BMI	4.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
entinostat	decreases expression, affects cotreatment	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
trichostatin A	decreases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	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, affects cotreatment	1
(+)-JQ1 compound	increases expression	1
Benzo(a)pyrene	increases methylation	1
Caffeine	decreases phosphorylation	1
Cisplatin	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects binding, increases expression	1
Melphalan	decreases expression	1
Quercetin	decreases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	affects methylation	1
Asbestos, Serpentine	decreases methylation	1

Clinical trials (associated diseases)

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