SWT1

Summary

SWT1 (SWT1 RNA endoribonuclease homolog, HGNC:16785) is a protein-coding gene on chromosome 1q25.3, encoding Transcriptional protein SWT1 (Q5T5J6).

Predicted to be active in nucleus.

Source: NCBI Gene 54823 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 134 total
• MANE Select transcript: NM_017673

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16785
Approved symbol	SWT1
Name	SWT1 RNA endoribonuclease homolog
Location	1q25.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20121, HsSwt1
Ensembl gene	ENSG00000116668
Ensembl biotype	protein_coding
OMIM	619513
Entrez	54823

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 20 protein_coding

ENST00000367500, ENST00000367501, ENST00000450350, ENST00000860004, ENST00000860005, ENST00000860006, ENST00000860007, ENST00000860008, ENST00000860009, ENST00000860010, ENST00000860011, ENST00000932220, ENST00000932221, ENST00000932222, ENST00000932223, ENST00000932224, ENST00000952356, ENST00000952357, ENST00000952358, ENST00000952359

RefSeq mRNA: 2 — MANE Select: NM_017673 NM_001105518, NM_017673

CCDS: CCDS1367

Canonical transcript exons

ENST00000367500 — 19 exons

Exon	Start	End
ENSE00000790763	185276604	185276668
ENSE00000822942	185206625	185206763
ENSE00000822943	185214507	185214655
ENSE00000822944	185221849	185222036
ENSE00000822948	185231577	185231708
ENSE00000822949	185271323	185271389
ENSE00000922205	185181946	185182057
ENSE00000959346	185180391	185180450
ENSE00000959347	185184243	185184344
ENSE00000959348	185184743	185184931
ENSE00000959349	185190549	185190642
ENSE00000959350	185202654	185202799
ENSE00000959351	185204700	185204863
ENSE00001127877	185174372	185175113
ENSE00001127885	185168340	185168398
ENSE00001127892	185166572	185166652
ENSE00001353785	185157167	185157314
ENSE00001444775	185290674	185291781
ENSE00001444785	185160833	185160925

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 93.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.1124 / max 108.5483, expressed in 1666 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
7248	2.0886	965
7249	1.7462	950
7247	1.4458	731
7246	0.4075	192
7245	0.2396	70
7250	0.1252	40
7244	0.0530	9
7243	0.0063	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.51	gold quality
secondary oocyte	CL:0000655	92.80	gold quality
calcaneal tendon	UBERON:0003701	88.18	gold quality
oocyte	CL:0000023	87.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.03	gold quality
left testis	UBERON:0004533	85.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.01	gold quality
right testis	UBERON:0004534	84.70	gold quality
testis	UBERON:0000473	84.43	gold quality
sural nerve	UBERON:0015488	82.00	gold quality
cortical plate	UBERON:0005343	81.60	gold quality
body of pancreas	UBERON:0001150	80.78	gold quality
tibialis anterior	UBERON:0001385	80.21	silver quality
ganglionic eminence	UBERON:0004023	80.05	gold quality
left ventricle myocardium	UBERON:0006566	79.68	gold quality
pancreas	UBERON:0001264	78.21	gold quality
ileal mucosa	UBERON:0000331	77.86	gold quality
bone marrow cell	CL:0002092	77.80	gold quality
ventricular zone	UBERON:0003053	77.37	gold quality
monocyte	CL:0000576	77.14	gold quality
deltoid	UBERON:0001476	77.12	silver quality
leukocyte	CL:0000738	76.96	gold quality
bone marrow	UBERON:0002371	76.80	gold quality
corpus callosum	UBERON:0002336	76.32	gold quality
islet of Langerhans	UBERON:0000006	75.41	gold quality
trabecular bone tissue	UBERON:0002483	74.96	gold quality
adrenal tissue	UBERON:0018303	74.50	gold quality
smooth muscle tissue	UBERON:0001135	74.38	gold quality
adult organism	UBERON:0007023	74.29	gold quality
colonic epithelium	UBERON:0000397	74.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting SWT1, 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-1277-5P	100.00	73.95	5056
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6744-5P	99.93	66.82	748
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-609	99.82	64.26	505
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-4645-3P	99.76	69.33	993
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-494-3P	99.70	71.45	2795

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	swt1	ENSDARG00000094010
mus_musculus	Swt1	ENSMUSG00000052748
rattus_norvegicus	Swt1	ENSRNOG00000032258
drosophila_melanogaster	Swt1	FBGN0030892
caenorhabditis_elegans		WBGENE00022883

Protein

Protein identifiers

Transcriptional protein SWT1 — Q5T5J6 (reviewed: Q5T5J6)

All UniProt accessions (2): Q5T5J6, Q5TC96

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Expressed weakly in testis.

Similarity. Belongs to the SWT1 family.

RefSeq proteins (2): NP_001098988, NP_060143* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002716	PIN_dom	Domain
IPR029060	PIN-like_dom_sf	Homologous_superfamily
IPR052626	SWT1_Regulator	Family

Pfam: PF13638

UniProt features (12 total): sequence variant 4, compositionally biased region 3, sequence conflict 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T5J6-F1	60.89	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): TGCGCANK_UNKNOWN, RACCACAR_AML_Q6, CHANDRAN_METASTASIS_DN, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, AML1_01, RGAGGAARY_PU1_Q6, YAMAZAKI_TCEB3_TARGETS_DN, OSF2_Q6, chr1q25, PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN, CIITA_TARGET_GENES, HES4_TARGET_GENES, HHEX_TARGET_GENES, SUPT16H_TARGET_GENES, ZIM3_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

680 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SWT1	IVNS1ABP	Q9Y6Y0	532
SWT1	SMG5	Q9UPR3	528
SWT1	TRMT1L	Q7Z2T5	520
SWT1	FMR1NB	Q8N0W7	500
SWT1	PHTF1	Q9UMS5	488
SWT1	TRIML2	Q8N7C3	476
SWT1	GRAMD4	Q6IC98	471
SWT1	PSMC3IP	Q9P2W1	456
SWT1	COQ3	Q9NZJ6	452
SWT1	AGTRAP	Q6RW13	445
SWT1	MAGEB17	A8MXT2	445
SWT1	GTF2H5	Q6ZYL4	443
SWT1	DMRTB1	Q96MA1	432
SWT1	RNF2	Q99496	409
SWT1	DIS3	Q9Y2L1	388

IntAct

3 interactions, top by confidence:

A	B	Type	Score
P		psi-mi:“MI:0914”(association)	0.350
ATG16L1		psi-mi:“MI:0914”(association)	0.350

BioGRID (8): SWT1 (Reconstituted Complex), SWT1 (Affinity Capture-MS), SWT1 (Synthetic Lethality), SWT1 (Affinity Capture-RNA), SWT1 (Cross-Linking-MS (XL-MS)), SWT1 (Protein-RNA), SWT1 (Cross-Linking-MS (XL-MS)), SWT1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0M3U1B0, A0A1L8EYB2, A0JMF7, A1L2Y1, A2ALV5, A9JRX0, B2GUZ2, D3ZSP7, F1QB81, O35892, O70608, O75113, P23497, P70347, Q0P5X5, Q13129, Q16533, Q2T9I9, Q3U1D0, Q5CZC0, Q5H9M0, Q5REF4, Q5RHB5, Q5SW75, Q5T4T6, Q5T5J6, Q5XG69, Q5ZLE9, Q60664, Q63HN8, Q7M6U3, Q7Z4H7, Q80VH0, Q8BVK9, Q8C263, Q8CCC3, Q8NA03, Q90WN7, Q92844, Q96QP1

Diamond homologs: Q5T5J6, Q9DBQ9, Q9P7J1, P61406, Q5RAK6, Q86US8, Q12104

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	96
Likely benign	16
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3946 predictions. Top by Δscore:

Variant	Effect	Δscore
1:185160919:TGAAA:T	donor_gain	1.0000
1:185160920:GAAAA:G	donor_gain	1.0000
1:185160921:AAAAA:A	donor_gain	1.0000
1:185160926:G:GG	donor_gain	1.0000
1:185166561:T:TA	acceptor_gain	1.0000
1:185166564:A:AG	acceptor_gain	1.0000
1:185166565:T:G	acceptor_gain	1.0000
1:185166567:CTTA:C	acceptor_loss	1.0000
1:185166568:TTA:T	acceptor_loss	1.0000
1:185166569:TA:T	acceptor_loss	1.0000
1:185166570:A:AG	acceptor_gain	1.0000
1:185166570:A:AT	acceptor_loss	1.0000
1:185166570:AG:A	acceptor_gain	1.0000
1:185166571:G:GG	acceptor_gain	1.0000
1:185166571:GG:G	acceptor_gain	1.0000
1:185166571:GGA:G	acceptor_gain	1.0000
1:185166571:GGAC:G	acceptor_gain	1.0000
1:185166648:AACTG:A	donor_gain	1.0000
1:185166649:ACTG:A	donor_gain	1.0000
1:185166650:CTG:C	donor_gain	1.0000
1:185166651:TG:T	donor_gain	1.0000
1:185166652:GG:G	donor_gain	1.0000
1:185166652:GGTG:G	donor_loss	1.0000
1:185166653:G:GC	donor_loss	1.0000
1:185166653:G:GG	donor_gain	1.0000
1:185166654:TGAG:T	donor_loss	1.0000
1:185166655:GAGT:G	donor_loss	1.0000
1:185168333:A:AG	acceptor_gain	1.0000
1:185168335:TTCA:T	acceptor_loss	1.0000
1:185168336:TCA:T	acceptor_loss	1.0000

AlphaMissense

5984 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:185184282:A:T	D393V	0.997
1:185184772:T:A	W424R	0.997
1:185184772:T:C	W424R	0.997
1:185184791:T:C	L430P	0.997
1:185202678:A:C	K516N	0.997
1:185202678:A:T	K516N	0.997
1:185206646:T:A	W619R	0.997
1:185206646:T:C	W619R	0.997
1:185184276:T:A	V391D	0.996
1:185184770:C:G	P423R	0.996
1:185190579:G:C	R487P	0.996
1:185184282:A:C	D393A	0.995
1:185184770:C:A	P423H	0.995
1:185190585:T:C	L489P	0.995
1:185202668:T:C	L513S	0.995
1:185202677:A:T	K516I	0.995
1:185184285:C:T	T394I	0.994
1:185190573:A:T	D485V	0.994
1:185190638:T:C	C507R	0.994
1:185204843:T:C	F605L	0.994
1:185204845:T:A	F605L	0.994
1:185204845:T:G	F605L	0.994
1:185204855:T:A	W609R	0.994
1:185204855:T:C	W609R	0.994
1:185190573:A:C	D485A	0.993
1:185190595:T:G	C492W	0.993
1:185202659:A:C	D510A	0.993
1:185202659:A:T	D510V	0.993
1:185206697:T:C	F636L	0.993
1:185206699:T:A	F636L	0.993

dbSNP variants (sampled 300 via entrez): RS1000002322 (1:185287028 A>G), RS1000014549 (1:185251629 G>C), RS1000023157 (1:185270942 A>G), RS1000038501 (1:185157720 T>C), RS1000049459 (1:185239234 C>G), RS1000052531 (1:185245411 A>T), RS1000084928 (1:185239037 C>T), RS1000101375 (1:185239032 C>G), RS1000104412 (1:185244023 A>G), RS1000112858 (1:185158068 A>G), RS1000126024 (1:185193571 A>G), RS1000138030 (1:185157436 C>T), RS1000202375 (1:185291568 G>A,T), RS1000208652 (1:185280413 C>T), RS1000232756 (1:185207563 C>T)

Disease associations

OMIM: gene MIM:619513 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): megacolon (MONDO:0001273)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002935_15	Lead levels	5.000000e-06
GCST009543_3	Cleft lip with or without cleft palate x maternal periconceptional vitamin use interaction (parent of origin effect)	9.000000e-06
GCST011122_31	Walking pace	1.000000e-08

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003959	cleft lip
EFO:0005939	parental genotype effect measurement
EFO:0009116	vitamin supplement exposure measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008531	Megacolon	C06.405.469.158.701

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	3
Cyclosporine	increases expression	3
Cadmium Chloride	increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
alpha-pinene	increases expression, increases abundance, affects cotreatment	1
bisphenol A	decreases methylation	1
trichostatin A	affects expression	1
sulforaphane	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
3-deazaneplanocin	decreases expression	1
phenethyl isothiocyanate	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
tacedinaline	increases expression	1
(+)-JQ1 compound	increases expression	1
Decitabine	affects expression	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Antimycin A	decreases expression	1
Arsenic	affects methylation	1
Cisplatin	affects expression	1
Doxorubicin	decreases expression	1
Estradiol	decreases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Dihydrotestosterone	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04340856	Not specified	COMPLETED	Retrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892	Not specified	NOT_YET_RECRUITING	Preoperative Fish Oil PN and Prognosis After Constipation Surgery