ZSWIM9

Summary

ZSWIM9 (zinc finger SWIM-type containing 9, HGNC:34495) is a protein-coding gene on chromosome 19q13.33, encoding Uncharacterized protein ZSWIM9 (Q86XI8).

Predicted to act upstream of or within hematopoietic progenitor cell differentiation.

Source: NCBI Gene 374920 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• MANE Select transcript: NM_199341

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34495
Approved symbol	ZSWIM9
Name	zinc finger SWIM-type containing 9
Location	19q13.33
Locus type	gene with protein product
Status	Approved
Aliases	LOC374920
Ensembl gene	ENSG00000185453
Ensembl biotype	protein_coding
Entrez	374920

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000328759, ENST00000593921, ENST00000614654, ENST00000884363, ENST00000884364, ENST00000884365, ENST00000884366

RefSeq mRNA: 1 — MANE Select: NM_199341 NM_199341

CCDS: CCDS74411

Canonical transcript exons

ENST00000614654 — 4 exons

Exon	Start	End
ENSE00001336247	48182455	48182767
ENSE00001336251	48171794	48172077
ENSE00003712466	48194653	48197620
ENSE00003847890	48170680	48170714

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 97.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 1.5770 / max 28.7072, expressed in 1123 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
208884	1.5770	1123

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	97.82	gold quality
upper arm skin	UBERON:0004263	97.37	gold quality
kidney epithelium	UBERON:0004819	96.53	gold quality
cerebellar vermis	UBERON:0004720	95.19	gold quality
left ventricle myocardium	UBERON:0006566	95.12	gold quality
vena cava	UBERON:0004087	94.81	gold quality
medial globus pallidus	UBERON:0002477	94.58	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.16	gold quality
nasal cavity epithelium	UBERON:0005384	94.08	silver quality
globus pallidus	UBERON:0001875	93.75	gold quality
myocardium	UBERON:0002349	93.48	silver quality
cardiac muscle of right atrium	UBERON:0003379	93.37	silver quality
parotid gland	UBERON:0001831	92.10	gold quality
body of tongue	UBERON:0011876	92.06	gold quality
cardia of stomach	UBERON:0001162	90.70	gold quality
lateral nuclear group of thalamus	UBERON:0002736	90.30	gold quality
sperm	CL:0000019	89.78	gold quality
tongue	UBERON:0001723	89.70	gold quality
dorsal plus ventral thalamus	UBERON:0001897	89.69	gold quality
subthalamic nucleus	UBERON:0001906	89.69	gold quality
pons	UBERON:0000988	89.66	gold quality
lateral globus pallidus	UBERON:0002476	89.62	gold quality
epithelial cell of pancreas	CL:0000083	89.56	silver quality
pylorus	UBERON:0001166	89.30	gold quality
ventral tegmental area	UBERON:0002691	89.23	gold quality
vastus lateralis	UBERON:0001379	89.14	silver quality
pericardium	UBERON:0002407	89.11	gold quality
pharyngeal mucosa	UBERON:0000355	88.86	gold quality
inferior vagus X ganglion	UBERON:0005363	88.69	gold quality
trachea	UBERON:0003126	88.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting ZSWIM9, 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-9-5P	100.00	72.28	2361
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-516A-3P	99.46	67.96	1378
HSA-MIR-516B-3P	99.46	67.96	1378
HSA-MIR-6513-5P	99.43	67.81	1071
HSA-MIR-1912-3P	99.32	67.40	936
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-1295B-5P	99.03	67.50	810
HSA-MIR-4290	98.51	65.17	907
HSA-MIR-5089-5P	98.45	66.06	1388
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-4469	97.93	65.81	1319
HSA-MIR-7111-3P	97.80	66.75	1467
HSA-MIR-6728-5P	97.79	66.33	891
HSA-MIR-4723-3P	97.67	65.91	1017
HSA-MIR-450B-3P	97.56	66.12	512
HSA-MIR-6769B-3P	97.41	65.53	1036
HSA-MIR-3183	97.40	65.68	978

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zswim9	ENSMUSG00000070814
rattus_norvegicus	Zswim9	ENSRNOG00000014186

Paralogs (3): SIAH2 (ENSG00000181788), SIAH1 (ENSG00000196470), SIAH3 (ENSG00000215475)

Protein

Protein identifiers

Uncharacterized protein ZSWIM9 — Q86XI8 (reviewed: Q86XI8)

All UniProt accessions (1): Q86XI8

UniProt curated annotations — full annotation on UniProt →

Isoforms (2)

UniProt ID	Names	Canonical?
Q86XI8-1	1	yes
Q86XI8-2	2

RefSeq proteins (1): NP_955373* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR040854	ZSWIM9	Family
IPR048315	ZSWIM9_RNaseH-like	Domain
IPR049217	DUF5575_N	Domain
IPR049218	DUF5575_C	Domain

Pfam: PF17738, PF20783, PF20784

UniProt features (6 total): region of interest 2, chain 1, compositionally biased region 1, splice variant 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XI8-F1	68.99	0.34

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): 807

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): E2F4DP1_01, E2F_Q3, MCAATNNNNNGCG_UNKNOWN, HIF1_Q3, E2F_Q6_01, ACTWSNACTNY_UNKNOWN, TCCCRNNRTGC_UNKNOWN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, MTF1_Q4, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, CHAF1B_TARGET_GENES, HOXB4_TARGET_GENES, HOXC6_TARGET_GENES, HOXD11_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (2): protein binding (GO:0005515), zinc ion binding (GO:0008270)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
transition metal ion binding	1

Protein interactions and networks

STRING

202 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZSWIM9	ZSWIM1	Q9BR11	732
ZSWIM9	CABP5	Q9NP86	518
ZSWIM9	ZSWIM5	Q9P217	497
ZSWIM9	MAP3K1	Q13233	469
ZSWIM9	ELSPBP1	Q96BH3	417
ZSWIM9	ZNF575	Q86XF7	402
ZSWIM9	PLA2G4C	Q9UP65	391
ZSWIM9	PHLDB3	Q6NSJ2	371
ZSWIM9	KDELR1	P24390	359
ZSWIM9	CARD8	Q9Y2G2	350
ZSWIM9	LIG1	P18858	314
ZSWIM9	SULT2A1	Q06520	305
ZSWIM9	GRIN2D	O15399	302
ZSWIM9	ZSWIM6	Q9HCJ5	289
ZSWIM9	ZSWIM4	Q9H7M6	289

IntAct

24 interactions, top by confidence:

A	B	Type	Score
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
DYNLL2	BLTP3B	psi-mi:“MI:0914”(association)	0.640
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
CBX1	ZNF292	psi-mi:“MI:0914”(association)	0.530
ZMYM4	ILVBL	psi-mi:“MI:0914”(association)	0.530
ZSWIM9	JUNB	psi-mi:“MI:0915”(physical association)	0.520
ESR2	FBLL1	psi-mi:“MI:0914”(association)	0.460
WAPL	RPL10	psi-mi:“MI:0914”(association)	0.350
Tp53bp1	WBP2	psi-mi:“MI:0914”(association)	0.350
WTAP	DDX39A	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
PTGES3	SBNO1	psi-mi:“MI:0914”(association)	0.350
NOL4	ZNF195	psi-mi:“MI:0914”(association)	0.350
CBX3	ZNF324	psi-mi:“MI:0914”(association)	0.350
FHL3		psi-mi:“MI:0914”(association)	0.350
AFG2A	ESYT2	psi-mi:“MI:0914”(association)	0.350
CBX3	MYL12B	psi-mi:“MI:0914”(association)	0.350
ZMYM2	ZBTB5	psi-mi:“MI:2364”(proximity)	0.270
ZMYM2	TRIM24	psi-mi:“MI:2364”(proximity)	0.270
ZMYM3	TAF4	psi-mi:“MI:2364”(proximity)	0.270
ZSWIM9	JUNB	psi-mi:“MI:0915”(physical association)	0.000
ZSWIM9	phnI	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (25): C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), SCAI (Affinity Capture-MS), CBX1 (Affinity Capture-MS), DNAJC9 (Affinity Capture-MS), ADNP2 (Affinity Capture-MS), C19orf68 (Affinity Capture-RNA), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS), C19orf68 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUU1, A2CI34, A4IG61, E9QAM5, O95248, O95398, P29597, P52333, Q14147, Q14689, Q17QP1, Q29S07, Q2KI13, Q2T9T9, Q3TL44, Q3UAW9, Q4R318, Q4V8D6, Q4VSN1, Q5FVQ8, Q62137, Q63272, Q6B0B8, Q6DI92, Q6ZPE2, Q6ZPG2, Q6ZPS2, Q7TM95, Q86UT6, Q86XI8, Q8BH02, Q8BH83, Q8BWT5, Q8C828, Q8CFL8, Q8K4K2, Q8N159, Q8R4H7, Q8VCC8, Q96KV7

Diamond homologs: Q6DI92, Q86XI8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

632 predictions. Top by Δscore:

Variant	Effect	Δscore
19:48172011:TGCTC:T	donor_gain	1.0000
19:48172024:C:G	donor_gain	1.0000
19:48172045:GGAC:G	donor_gain	1.0000
19:48172046:GACG:G	donor_gain	1.0000
19:48194638:T:TA	acceptor_gain	1.0000
19:48194644:C:A	acceptor_gain	1.0000
19:48194651:A:AG	acceptor_gain	1.0000
19:48194651:AG:A	acceptor_gain	1.0000
19:48194651:AGGT:A	acceptor_gain	1.0000
19:48194652:G:GT	acceptor_gain	1.0000
19:48194652:GG:G	acceptor_gain	1.0000
19:48194652:GGT:G	acceptor_gain	1.0000
19:48194652:GGTG:G	acceptor_gain	1.0000
19:48194652:GGTGA:G	acceptor_gain	1.0000
19:48171788:A:AG	acceptor_gain	0.9900
19:48171788:AC:A	acceptor_gain	0.9900
19:48171789:C:CA	acceptor_gain	0.9900
19:48171789:C:G	acceptor_gain	0.9900
19:48171791:CA:C	acceptor_loss	0.9900
19:48171792:A:AG	acceptor_gain	0.9900
19:48171792:AG:A	acceptor_gain	0.9900
19:48171793:G:GA	acceptor_gain	0.9900
19:48171793:GG:G	acceptor_gain	0.9900
19:48171793:GGC:G	acceptor_gain	0.9900
19:48171793:GGCC:G	acceptor_gain	0.9900
19:48171793:GGCCC:G	acceptor_gain	0.9900
19:48172012:GCTCA:G	donor_gain	0.9900
19:48172018:G:GG	donor_gain	0.9900
19:48172116:G:T	donor_gain	0.9900
19:48182450:CACA:C	acceptor_loss	0.9900

AlphaMissense

5878 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:48171872:T:C	F24L	1.000
19:48171874:C:A	F24L	1.000
19:48171874:C:G	F24L	1.000
19:48171881:T:A	W27R	1.000
19:48171881:T:C	W27R	1.000
19:48171883:G:C	W27C	1.000
19:48171883:G:T	W27C	1.000
19:48171891:T:C	F30S	1.000
19:48172035:T:C	L78P	1.000
19:48172040:T:C	C80R	1.000
19:48172041:G:A	C80Y	1.000
19:48172042:C:G	C80W	1.000
19:48182517:T:A	L113H	1.000
19:48182517:T:C	L113P	1.000
19:48182570:T:C	F131L	1.000
19:48182572:C:A	F131L	1.000
19:48182572:C:G	F131L	1.000
19:48182651:T:C	F158L	1.000
19:48182652:T:C	F158S	1.000
19:48182652:T:G	F158C	1.000
19:48182653:C:A	F158L	1.000
19:48182653:C:G	F158L	1.000
19:48194665:T:C	F201L	1.000
19:48194666:T:C	F201S	1.000
19:48194667:C:A	F201L	1.000
19:48194667:C:G	F201L	1.000
19:48194881:T:C	F273L	1.000
19:48194883:C:A	F273L	1.000
19:48194883:C:G	F273L	1.000
19:48171873:T:C	F24S	0.999

dbSNP variants (sampled 300 via entrez): RS1000004962 (19:48182503 G>A), RS1000013643 (19:48183367 T>C), RS1000025107 (19:48179140 AT>A,ATT,ATTTT), RS1000048604 (19:48171696 G>A,T), RS1000071585 (19:48183489 G>A,C), RS1000135016 (19:48173567 C>T), RS1000149587 (19:48176191 G>C), RS1000163183 (19:48170734 A>G), RS1000166707 (19:48174990 T>C), RS1000175723 (19:48188458 G>T), RS1000226177 (19:48178825 C>T), RS1000411636 (19:48194274 C>T), RS1000798382 (19:48189008 G>T), RS1001266981 (19:48175963 T>C), RS1001582415 (19:48193039 G>A)

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

1 associations (top):

Study	Trait	p-value
GCST009391_1675	Metabolite levels	9.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010340	cholesteryl ester 14:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
sodium arsenite	increases expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Thiram	increases expression	1
Tobacco Smoke Pollution	decreases methylation	1
Valproic Acid	increases methylation	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cadmium Chloride	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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