SPATS2L

Summary

SPATS2L (spermatogenesis associated serine rich 2 like, HGNC:24574) is a protein-coding gene on chromosome 2q33.1, encoding SPATS2-like protein (Q9NUQ6).

Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex.

Source: NCBI Gene 26010 — RefSeq curated summary.

At a glance

• GWAS associations: 75
• Clinical variants (ClinVar): 103 total
• Druggable target: yes
• MANE Select transcript: NM_001100423

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24574
Approved symbol	SPATS2L
Name	spermatogenesis associated serine rich 2 like
Location	2q33.1
Locus type	gene with protein product
Status	Approved
Aliases	DNAPTP6, SGNP
Ensembl gene	ENSG00000196141
Ensembl biotype	protein_coding
OMIM	613817
Entrez	26010

Gene structure

Transcript identifiers

Ensembl transcripts: 94 — 88 protein_coding, 3 retained_intron, 3 protein_coding_CDS_not_defined

ENST00000358677, ENST00000360760, ENST00000366118, ENST00000409140, ENST00000409151, ENST00000409385, ENST00000409397, ENST00000409718, ENST00000409988, ENST00000421573, ENST00000423749, ENST00000428692, ENST00000438761, ENST00000439084, ENST00000439395, ENST00000444012, ENST00000449647, ENST00000451764, ENST00000453663, ENST00000457757, ENST00000459656, ENST00000460095, ENST00000462190, ENST00000468832, ENST00000471533, ENST00000471601, ENST00000619961, ENST00000891339, ENST00000891340, ENST00000891341, ENST00000891342, ENST00000891343, ENST00000891344, ENST00000891345, ENST00000891346, ENST00000891347, ENST00000891348, ENST00000891349, ENST00000891350, ENST00000891351, ENST00000891352, ENST00000891353, ENST00000891354, ENST00000891355, ENST00000891356, ENST00000891357, ENST00000891358, ENST00000891359, ENST00000891360, ENST00000891361, ENST00000891362, ENST00000891363, ENST00000891364, ENST00000891365, ENST00000891366, ENST00000891367, ENST00000932082, ENST00000932083, ENST00000932084, ENST00000932085, ENST00000932086, ENST00000932087, ENST00000932088, ENST00000932089, ENST00000932090, ENST00000932091, ENST00000932092, ENST00000932093, ENST00000932094, ENST00000932095, ENST00000932096, ENST00000932097, ENST00000932098, ENST00000932099, ENST00000932100, ENST00000932101, ENST00000932102, ENST00000958377, ENST00000958378, ENST00000958379, ENST00000958380, ENST00000958381, ENST00000958382, ENST00000958383, ENST00000958384, ENST00000958385, ENST00000958386, ENST00000958387, ENST00000958388, ENST00000958389, ENST00000958390, ENST00000958391, ENST00000958392, ENST00000958393

RefSeq mRNA: 7 — MANE Select: NM_001100423 NM_001100422, NM_001100423, NM_001100424, NM_001282735, NM_001282743, NM_001282744, NM_015535

CCDS: CCDS46483, CCDS46484, CCDS74621, CCDS74622

Canonical transcript exons

ENST00000409140 — 13 exons

Exon	Start	End
ENSE00001587002	200306693	200306922
ENSE00002274285	200419250	200419496
ENSE00002279474	200459769	200459827
ENSE00002286110	200439122	200439328
ENSE00003460589	200389223	200389283
ENSE00003510583	200469914	200470016
ENSE00003537166	200467290	200467399
ENSE00003574860	200412311	200412419
ENSE00003675401	200472832	200473052
ENSE00003683745	200329431	200329480
ENSE00003717155	200416379	200416428
ENSE00003784632	200440649	200440784
ENSE00003841470	200477636	200482264

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 99.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 50.8069 / max 642.6341, expressed in 1777 samples.

FANTOM5 promoters (20 alternative TSS)

Promoter ID	TPM avg	Samples expressed
24536	33.0078	1749
24535	8.6320	1618
24538	1.8415	1045
24537	1.5005	959
24533	1.3010	765
24534	1.2124	730
24544	1.0132	169
202532	0.5382	300
24528	0.3567	177
24545	0.3039	82

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	99.38	gold quality
parotid gland	UBERON:0001831	98.81	gold quality
metanephric glomerulus	UBERON:0004736	98.36	gold quality
gall bladder	UBERON:0002110	98.33	gold quality
renal glomerulus	UBERON:0000074	98.32	gold quality
tibia	UBERON:0000979	98.28	gold quality
stromal cell of endometrium	CL:0002255	98.14	gold quality
colonic mucosa	UBERON:0000317	97.75	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.62	gold quality
ileal mucosa	UBERON:0000331	97.57	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.56	gold quality
germinal epithelium of ovary	UBERON:0001304	97.54	gold quality
seminal vesicle	UBERON:0000998	97.47	gold quality
kidney epithelium	UBERON:0004819	97.47	gold quality
rectum	UBERON:0001052	97.37	gold quality
esophagus squamous epithelium	UBERON:0006920	97.31	gold quality
islet of Langerhans	UBERON:0000006	97.29	gold quality
nasal cavity mucosa	UBERON:0001826	97.25	gold quality
parietal pleura	UBERON:0002400	97.23	gold quality
periodontal ligament	UBERON:0008266	97.23	gold quality
tongue squamous epithelium	UBERON:0006919	97.22	gold quality
jejunal mucosa	UBERON:0000399	97.21	gold quality
cartilage tissue	UBERON:0002418	97.20	gold quality
nephron tubule	UBERON:0001231	97.05	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.00	gold quality
middle temporal gyrus	UBERON:0002771	96.94	gold quality
pleura	UBERON:0000977	96.90	gold quality
epithelium of esophagus	UBERON:0001976	96.84	gold quality
duodenum	UBERON:0002114	96.73	gold quality
nasal cavity epithelium	UBERON:0005384	96.73	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-GEOD-130473	yes	173.41
E-MTAB-6108	yes	134.47
E-HCAD-5	yes	33.14
E-GEOD-125970	yes	23.35
E-MTAB-10553	yes	22.74
E-ANND-3	yes	14.80
E-HCAD-9	yes	11.92
E-MTAB-8410	yes	3.85
E-GEOD-36552	no	167.46
E-HCAD-31	no	3.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

157 targeting SPATS2L, 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-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-101-3P	99.94	75.03	2230

Literature-anchored findings (GeneRIF, showing 7)

• SGNP is localized in both the cytoplasm and nucleolus and defines a non-nucleolar compartment containing 5.8S rRNA. Under oxidative stress, SGNP nucleolar localization decreases and it rapidly co-localizes with stress granules. (PMID:19005571)
• Our results suggest that SPATS2L may be an important regulator of beta(2)-adrenergic receptor down-regulation and that there is promise in gaining a better understanding of the biological mechanisms of differential response to beta(2)-agonists through GWAS. (PMID:22792082)
• A haplotype of 23 SNPs spanning 131.6 Kb shared by all affected members of 3 linked families with restless legs syndrome was identified. The shared candidate region covers 46.9 Kb over the potassium channel-related gene KCTD18 and exons 10-13 of SPATS2L. (PMID:23054586)
• Down-regulation of SPATS2L expression may be related to the etiology of poor sleep quality and chronic abdominal pain. (PMID:25358868)
• While controlling for clinical determinants, in acute asthma therapy response, SNP rs295137 in SPATS2L (OR = 1.77, 95%CI: 1.17, 2.68) was significantly associated with increased odds of emergency department (ED) management failure. Two SNPs in IL33 were associated with decreased odds of ED management failure: rs7037276 (OR = 0.55, 95%CI: 0.33, 0.90), and rs1342326 (OR = 0.52, 95%CI: 0.32, 0.86). (PMID:30644648)
• Respiratory traits and coal workers’ pneumoconiosis: Mendelian randomisation and association analysis. (PMID:33097673)
• Spermatogenesis associated serine rich 2 like plays a prognostic factor and therapeutic target in acute myeloid leukemia by regulating the JAK2/STAT3/STAT5 axis. (PMID:36774517)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spats2l	ENSMUSG00000038305
rattus_norvegicus	Spats2l	ENSRNOG00000016012
caenorhabditis_elegans	Y71F9AL.9	WBGENE00022114

Paralogs (1): SPATS2 (ENSG00000123352)

Protein

Protein identifiers

SPATS2-like protein — Q9NUQ6 (reviewed: Q9NUQ6)

Alternative names: DNA polymerase-transactivated protein 6, Stress granule and nucleolar protein

All UniProt accessions (14): B8ZZZ7, C9IZC3, C9J8M7, C9JGM8, C9JKE4, C9JW67, Q9NUQ6, F2Z2S1, F8VT91, F8VZ02, F8W6C2, F8WAV0, H7C2G5, Q4ZFW0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Nucleus. Nucleolus.

Similarity. Belongs to the SPATS2 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9NUQ6-1	1	yes
Q9NUQ6-2	2
Q9NUQ6-3	3
Q9NUQ6-4	4

RefSeq proteins (7): NP_001093892, NP_001093893, NP_001093894, NP_001269664, NP_001269672, NP_001269673, NP_056350 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009060	UBA-like_sf	Homologous_superfamily
IPR009816	SPATS2-like	Family

Pfam: PF07139

UniProt features (22 total): compositionally biased region 7, modified residue 3, splice variant 3, sequence conflict 3, region of interest 3, initiator methionine 1, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUQ6-F1	63.72	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 (3): 2, 120, 455

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 274 (showing top): TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP, HORIUCHI_WTAP_TARGETS_DN, XU_GH1_AUTOCRINE_TARGETS_UP, TTTGTAG_MIR520D, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GRYDER_PAX3FOXO1_TOP_ENHANCERS, GOCC_NUCLEOLUS, COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP, JIANG_VHL_TARGETS, CHEN_METABOLIC_SYNDROM_NETWORK, GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN, DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), protein-containing complex (GO:0032991), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
nuclear lumen	2
nucleic acid binding	1
binding	1
intracellular membraneless organelle	1
intracellular anatomical structure	1
cytoplasm	1
cellular_component	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

840 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATS2L	RTP4	Q96DX8	565
SPATS2L	KCTD18	Q6PI47	554
SPATS2L	EPSTI1	Q96J88	502
SPATS2L	FRMPD1	Q5SYB0	460
SPATS2L	TMEM51	Q9NW97	445
SPATS2L	TTC22	Q5TAA0	439
SPATS2L	CPNE5	Q9HCH3	433
SPATS2L	C2orf69	Q8N8R5	433
SPATS2L	GLCCI1	Q86VQ1	432
SPATS2L	IFI44L	Q53G44	432
SPATS2L	FTCDNL1	E5RQL4	431
SPATS2L	IFI44	Q8TCB0	427
SPATS2L	TYW5	A2RUC4	424
SPATS2L	MCTP2	Q6DN12	424
SPATS2L	CYRIA	Q9H0Q0	421

IntAct

117 interactions, top by confidence:

A	B	Type	Score
FANCC	FANCA	psi-mi:“MI:0914”(association)	0.680
LIN28A	IGF2BP3	psi-mi:“MI:0914”(association)	0.640
TRIM44	CUL2	psi-mi:“MI:0914”(association)	0.640
N	RBM47	psi-mi:“MI:0914”(association)	0.530
TRIM44	ODAD3	psi-mi:“MI:0914”(association)	0.530
LTBR	ZNF724	psi-mi:“MI:0914”(association)	0.530
MAGEB2	GTPBP10	psi-mi:“MI:0914”(association)	0.530
RPS2	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
KRR1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.530
GATAD1	SIN3B	psi-mi:“MI:0914”(association)	0.530
IFNA14	IFIT1	psi-mi:“MI:0914”(association)	0.530
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
SPATS2L	AP2A1	psi-mi:“MI:0915”(physical association)	0.400
SPATS2L	CUX1	psi-mi:“MI:0914”(association)	0.350
RPGRIP1L	KIF2A	psi-mi:“MI:0914”(association)	0.350
EBNA1	IGF2BP3	psi-mi:“MI:0914”(association)	0.350
KIE-1	GTPBP10	psi-mi:“MI:0914”(association)	0.350
Prdm16	ESYT2	psi-mi:“MI:0914”(association)	0.350
Mecom	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
FGFR1	POLRMT	psi-mi:“MI:0914”(association)	0.350
CTBP1	TAF15	psi-mi:“MI:0914”(association)	0.350
CTBP1	GSN	psi-mi:“MI:0914”(association)	0.350
N	POLRMT	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
N	RBM47	psi-mi:“MI:0914”(association)	0.350

BioGRID (165): SPATS2L (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), SPATS2L (Proximity Label-MS), CUX1 (Affinity Capture-MS), RAPGEF1 (Affinity Capture-MS), SET (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), PLXNA3 (Affinity Capture-MS), USMG5 (Affinity Capture-MS), SGOL2 (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), SPATS2L (Affinity Capture-MS), SPATS2L (Affinity Capture-MS)

ESM2 similar proteins: A5PJS6, A5PMR2, A8HAL1, E1C213, E2RK09, E7F6T8, E9QG68, F1N5V1, F1SRY5, O15164, O75151, O88974, P52479, Q0VA64, Q14694, Q15047, Q2NL57, Q3KR59, Q3UWM4, Q5JSH3, Q5U2T3, Q5ZJN4, Q64127, Q6DIJ4, Q6NVE8, Q6P1H6, Q6PAW2, Q6ZMT4, Q70CQ4, Q7TP65, Q7ZXR7, Q86T82, Q86XL3, Q8BW70, Q8C0R0, Q8CG79, Q8NB14, Q8TEW8, Q8WYQ5, Q91WJ7

Diamond homologs: Q5U2T3, Q86XZ4, Q8K1N4, Q91WJ7, Q9NUQ6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 137 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Eukaryotic Translation Initiation	7	22.3×	5e-07
Cap-dependent Translation Initiation	7	22.3×	5e-07
SARS-CoV-1 modulates host translation machinery	7	22.3×	5e-07
Peptide chain elongation	17	22.2×	1e-16
Viral mRNA Translation	17	22.2×	1e-16
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	17	22.0×	1e-16
Selenocysteine synthesis	17	21.1×	2e-16
Eukaryotic Translation Termination	17	21.1×	2e-16

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	18	27.3×	2e-18
ribosomal small subunit biogenesis	11	20.5×	2e-09
translation	19	16.0×	3e-15
negative regulation of translation	7	11.2×	6e-04
rRNA processing	8	9.3×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	84
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2823 predictions. Top by Δscore:

Variant	Effect	Δscore
2:200321304:T:TA	donor_gain	1.0000
2:200321305:A:AA	donor_gain	1.0000
2:200329425:TCCTA:T	acceptor_loss	1.0000
2:200329426:CCTA:C	acceptor_loss	1.0000
2:200329427:CTA:C	acceptor_loss	1.0000
2:200329428:TAGA:T	acceptor_loss	1.0000
2:200329430:G:T	acceptor_loss	1.0000
2:200329430:GA:G	acceptor_gain	1.0000
2:200383849:AT:A	acceptor_gain	1.0000
2:200383850:T:G	acceptor_gain	1.0000
2:200389219:ATAG:A	acceptor_gain	1.0000
2:200389221:A:AC	acceptor_loss	1.0000
2:200389221:A:AG	acceptor_gain	1.0000
2:200389221:AG:A	acceptor_gain	1.0000
2:200389221:AGG:A	acceptor_gain	1.0000
2:200389222:G:GG	acceptor_gain	1.0000
2:200389222:GG:G	acceptor_gain	1.0000
2:200389222:GGG:G	acceptor_gain	1.0000
2:200389222:GGGC:G	acceptor_gain	1.0000
2:200389282:AGG:A	donor_loss	1.0000
2:200389284:GTAA:G	donor_loss	1.0000
2:200389285:T:A	donor_loss	1.0000
2:200412305:TTACA:T	acceptor_loss	1.0000
2:200412306:TACA:T	acceptor_loss	1.0000
2:200412307:ACAG:A	acceptor_loss	1.0000
2:200412308:CAGAT:C	acceptor_loss	1.0000
2:200412309:A:AG	acceptor_gain	1.0000
2:200412309:A:T	acceptor_loss	1.0000
2:200412310:G:GG	acceptor_gain	1.0000
2:200419243:A:AG	acceptor_gain	1.0000

AlphaMissense

3690 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:200412321:T:A	V17D	1.000
2:200412324:G:C	R18T	1.000
2:200412325:A:C	R18S	1.000
2:200412325:A:T	R18S	1.000
2:200412330:T:A	V20D	1.000
2:200412333:T:A	V21D	1.000
2:200412357:T:A	I29K	1.000
2:200412357:T:G	I29R	1.000
2:200412360:T:A	V30D	1.000
2:200412363:T:C	L31P	1.000
2:200412366:T:A	V32E	1.000
2:200412369:T:A	L33H	1.000
2:200412369:T:C	L33P	1.000
2:200412398:G:C	A43P	1.000
2:200412399:C:A	A43D	1.000
2:200412407:G:C	A46P	1.000
2:200412411:T:C	F47S	1.000
2:200412411:T:G	F47C	1.000
2:200416397:T:C	L56P	1.000
2:200416405:T:A	W59R	1.000
2:200416405:T:C	W59R	1.000
2:200416406:G:C	W59S	1.000
2:200416407:G:C	W59C	1.000
2:200416407:G:T	W59C	1.000
2:200440675:G:C	D227H	1.000
2:200440676:A:G	D227G	1.000
2:200440679:T:C	L228S	1.000
2:200440684:C:A	R230S	1.000
2:200440685:G:C	R230P	1.000
2:200440700:T:C	L235P	1.000

dbSNP variants (sampled 300 via entrez): RS1000001328 (2:200475451 G>A), RS1000012982 (2:200439880 A>G), RS1000018079 (2:200452171 C>CT), RS1000055925 (2:200359800 T>G), RS1000083435 (2:200352062 A>G), RS1000086056 (2:200307349 GGC>G), RS1000124027 (2:200361412 G>A), RS1000128248 (2:200352268 A>G), RS1000134664 (2:200445797 T>C), RS1000170861 (2:200332930 A>C), RS1000171490 (2:200307837 G>C), RS1000183701 (2:200366479 T>C), RS1000207236 (2:200426210 C>T), RS1000209233 (2:200469706 T>C), RS1000234153 (2:200459457 G>A)

Disease associations

OMIM: gene MIM:613817 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

75 associations (top):

Study	Trait	p-value
GCST000474_1	Leisure-time exercise behaviour	8.000000e-06
GCST001597_1	Asthma (bronchodilator response)	1.000000e-06
GCST002149_16	Schizophrenia	1.000000e-08
GCST002500_31	QT interval	4.000000e-13
GCST002830_22	Urate levels in lean individuals	2.000000e-06
GCST003226_12	Pelvic organ prolapse	3.000000e-06
GCST003254_6	Urinary albumin-to-creatinine ratio in non-diabetics	9.000000e-06
GCST003499_2	Reaction time	3.000000e-08
GCST004031_2	QT interval (sulfonylurea treatment interaction)	3.000000e-07
GCST004521_125	Autism spectrum disorder or schizophrenia	3.000000e-12
GCST004757_3	Alcohol dependence or chronic alcoholic pancreatitis or alcohol-related liver cirrhosis	5.000000e-06
GCST004946_172	Schizophrenia	3.000000e-10
GCST004946_73	Schizophrenia	3.000000e-12
GCST006061_1	Atrial fibrillation	2.000000e-20
GCST006061_2	Atrial fibrillation	4.000000e-17
GCST006268_201	Reaction time	2.000000e-10
GCST006268_202	Reaction time	5.000000e-09
GCST006268_203	Reaction time	9.000000e-11
GCST006268_504	Reaction time	4.000000e-12
GCST006414_72	Atrial fibrillation	6.000000e-24
GCST006628_22	Systolic blood pressure	2.000000e-12
GCST006803_6	Schizophrenia	4.000000e-17
GCST007201_234	Schizophrenia	9.000000e-11
GCST007201_37	Schizophrenia	4.000000e-09
GCST007201_4	Schizophrenia	6.000000e-09
GCST007430_25	Peak expiratory flow	5.000000e-06
GCST007431_37	Lung function (FEV1/FVC)	6.000000e-10
GCST007432_7	FEV1	2.000000e-07
GCST007561_69	Sleep duration	2.000000e-08
GCST009524_121	Household income (MTAG)	3.000000e-08

EFO canonical traits (12, from GWAS)

EFO ID	Trait name
EFO:0000483	exercise
EFO:0004682	QT interval
EFO:0004531	urate measurement
EFO:0007778	urinary albumin to creatinine ratio
EFO:0008393	reaction time measurement
EFO:0007922	response to sulfonylurea
EFO:0006335	systolic blood pressure
EFO:0009718	peak expiratory flow
EFO:0004713	FEV/FVC ratio
EFO:0004314	forced expiratory volume
EFO:0009695	household income
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067166 (SINGLE PROTEIN)

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

PharmGKB variants

2 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs295114	SPATS2L		0.00	0
rs295137	SPATS2L		0.00	0

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.38	Kd	41.49	nM	CHEMBL3752910
7.38	ED50	41.49	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149943: Binding affinity to human SPATS2L incubated for 45 mins by Kinobead based pull down assay	kd	0.0415	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tretinoin	increases expression	4
Particulate Matter	increases expression, decreases expression, decreases reaction, affects cotreatment, increases abundance	4
sodium arsenite	increases expression, affects response to substance, affects localization, increases activity	3
Estradiol	increases expression	3
bisphenol A	decreases expression, decreases methylation	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	2
Acetaminophen	increases expression	2
Vehicle Emissions	decreases expression, decreases reaction, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Valproic Acid	affects expression, decreases methylation	2
Aflatoxin B1	affects cotreatment, decreases expression, decreases methylation	2
aristolochic acid I	decreases expression	1
sotorasib	affects cotreatment, decreases expression	1
pirinixic acid	increases expression, affects binding, increases activity	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, decreases expression	1
salinomycin	decreases expression	1
beta-lapachone	increases expression	1
sodium bichromate	decreases expression	1
cobaltous chloride	decreases expression	1
ochratoxin A	increases expression	1
isobutyl alcohol	affects cotreatment, increases abundance, increases expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation, decreases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
dorsomorphin	affects cotreatment, increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
bisphenol AF	increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652985	Binding	Binding affinity to human SPATS2L incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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