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 and nucleolus. Part of protein-containing complex.

Source: NCBI Gene 26010 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 75 (top 1% of genes corpus-wide)
• Clinical variants (ClinVar): 104 total
• GTEx eGene: eQTL in 22 tissues, sQTL in 18 (q < 0.05)
• Constraint (gnomAD): pLI 0.01 (LoF-tolerant), LOEUF 0.72 (unconstrained)
• MANE Select transcript: NM_001100423
• Notable: 104 clinical variants but no curated precision-oncology (CIViC) evidence yet

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: 108 — 96 protein_coding, 6 nonsense_mediated_decay, 3 retained_intron, 3 protein_coding_CDS_not_defined

MANE Select: ENST00000409140

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 8, TSL 3: 5, TSL 4: 4, TSL 5: 7

ENST00000409140, ENST00000358677, ENST00000360760, ENST00000366118, 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, ENST00000989767, ENST00001056038, ENST00001056039, ENST00001056040, ENST00001056041, ENST00001056042, ENST00001056043, ENST00001088711, ENST00001108939, ENST00001108940, ENST00001108941, ENST00001108942, ENST00001122673, ENST00001122674

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
ENSE00004805417	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.

Highest expression (Bgee): pancreatic ductal cell, parotid gland, metanephric glomerulus, gall bladder, renal glomerulus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

SPATS2L is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 22 tissues and its splicing (sQTL) in 18 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 40 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells Cultured fibroblasts	sqtl	1.0e-54	+2.00	2:200308897:A:G
Esophagus Mucosa	sqtl	7.7e-35	+1.73	2:200311348:C:T
Skin Sun Exposed Lower leg	eqtl	6.9e-26	+0.37	2:200297541:G:GA
Thyroid	eqtl	3.0e-22	-0.37	2:200251711:A:G
Thyroid	sqtl	3.3e-22	+1.45	2:200326799:C:T
Lung	sqtl	1.7e-20	+1.50	2:200308897:A:G
Skin Not Sun Exposed Suprapubic	eqtl	1.0e-19	+0.32	2:200301737:C:CTT
Adipose Visceral Omentum	sqtl	8.2e-19	+1.42	2:200308897:A:G
Esophagus Muscularis	eqtl	1.2e-18	+0.30	2:200336095:A:G
Heart Atrial Appendage	eqtl	1.6e-18	-0.30	2:200306746:CTG:C
Esophagus Gastroesophageal Junction	eqtl	1.0e-13	+0.36	2:200336095:A:G
Testis	eqtl	3.9e-12	+0.23	2:200312178:C:T
Testis	sqtl	6.3e-10	+1.23	2:200311348:C:T
Heart Left Ventricle	eqtl	8.8e-10	-0.20	2:200298731:A:T
Colon Transverse	sqtl	3.0e-09	+1.13	2:200308897:A:G
Cells EBV-transformed lymphocytes	eqtl	2.6e-08	-0.33	2:200466707:T:G
Artery Tibial	eqtl	1.1e-06	+0.24	2:200336467:T:G
Skin Sun Exposed Lower leg	sqtl	6.0e-06	-0.35	2:200308276:C:T
Brain Cerebellar Hemisphere	sqtl	1.5e-05	+0.57	2:200211678:A:G
Whole Blood	eqtl	3.5e-05	+0.14	2:200306632:T:C

FANTOM5 promoters

showing 10 of 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

showing 100 of 288 tissues 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
palpebral conjunctiva	UBERON:0001812	96.69	gold quality
epithelial cell of pancreas	CL:0000083	96.61	gold quality
left ventricle myocardium	UBERON:0006566	96.53	gold quality
decidua	UBERON:0002450	96.47	gold quality
metanephros	UBERON:0000081	96.45	gold quality
visceral pleura	UBERON:0002401	96.38	gold quality
trachea	UBERON:0003126	96.23	gold quality
squamous epithelium	UBERON:0006914	96.19	gold quality
right uterine tube	UBERON:0001302	96.12	gold quality
myocardium	UBERON:0002349	96.09	gold quality
adult mammalian kidney	UBERON:0000082	96.08	gold quality
saliva-secreting gland	UBERON:0001044	96.04	gold quality
bronchus	UBERON:0002185	95.99	gold quality
epithelium of bronchus	UBERON:0002031	95.98	gold quality
jejunum	UBERON:0002115	95.87	gold quality
mammalian vulva	UBERON:0000997	95.86	gold quality
large intestine	UBERON:0000059	95.84	gold quality
kidney	UBERON:0002113	95.84	gold quality
mucosa of transverse colon	UBERON:0004991	95.83	gold quality
cardiac atrium	UBERON:0002081	95.81	gold quality
colon	UBERON:0001155	95.78	gold quality
bronchial epithelial cell	CL:0002328	95.73	gold quality
right atrium auricular region	UBERON:0006631	95.66	gold quality
liver	UBERON:0002107	95.60	gold quality
transverse colon	UBERON:0001157	95.49	gold quality
left uterine tube	UBERON:0001303	95.49	gold quality
intestine	UBERON:0000160	95.38	gold quality
smooth muscle tissue	UBERON:0001135	95.38	gold quality
mucosa of urinary bladder	UBERON:0001259	95.36	gold quality
minor salivary gland	UBERON:0001830	95.36	gold quality
epithelium of nasopharynx	UBERON:0001951	95.33	gold quality
mouth mucosa	UBERON:0003729	95.33	gold quality
saphenous vein	UBERON:0007318	95.25	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.24	gold quality
gingiva	UBERON:0001828	95.23	gold quality
urinary bladder	UBERON:0001255	95.22	gold quality
uterine cervix	UBERON:0000002	95.20	gold quality
upper leg skin	UBERON:0004262	95.12	gold quality
upper arm skin	UBERON:0004263	95.12	gold quality
hair follicle	UBERON:0002073	95.11	gold quality
amniotic fluid	UBERON:0000173	95.10	gold quality
endocervix	UBERON:0000458	95.10	gold quality
gingival epithelium	UBERON:0001949	94.97	gold quality
urethra	UBERON:0000057	94.94	gold quality
Brodmann (1909) area 23	UBERON:0013554	94.93	gold quality
ectocervix	UBERON:0012249	94.87	gold quality
muscle tissue	UBERON:0002385	94.85	gold quality
heart	UBERON:0000948	94.80	gold quality
pancreas	UBERON:0001264	94.74	gold quality
mucosa of paranasal sinus	UBERON:0005030	94.73	gold quality
deltoid	UBERON:0001476	94.70	gold quality
calcaneal tendon	UBERON:0003701	94.68	gold quality
vena cava	UBERON:0004087	94.68	gold quality
right lung	UBERON:0002167	94.63	gold quality
cortex of kidney	UBERON:0001225	94.61	gold quality
heart left ventricle	UBERON:0002084	94.48	gold quality
placenta	UBERON:0001987	94.47	gold quality
cardiac ventricle	UBERON:0002082	94.42	gold quality
quadriceps femoris	UBERON:0001377	94.40	gold quality
right lobe of liver	UBERON:0001114	94.39	gold quality
cervix epithelium	UBERON:0004801	94.38	gold quality
popliteal artery	UBERON:0002250	94.36	gold quality
tibial artery	UBERON:0007610	94.35	gold quality
skeletal muscle tissue	UBERON:0001134	94.33	gold quality
adult organism	UBERON:0007023	94.33	gold quality
pylorus	UBERON:0001166	94.30	gold quality
vastus lateralis	UBERON:0001379	94.23	gold quality
hindlimb stylopod muscle	UBERON:0004252	94.23	gold quality
olfactory bulb	UBERON:0002264	94.20	gold quality
esophagus mucosa	UBERON:0002469	94.20	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Salivary gland	tissue	156.4	high
Heart muscle	tissue	109.8	medium
Gallbladder	tissue	107.5	high
Liver	tissue	103.1	medium
Stomach 1	tissue	95.7	medium
Colon	tissue	80.1	medium
Rectum	tissue	77.9	high
Small intestine	tissue	77.9	high
Duodenum	tissue	77.3	high
Fallopian tube	tissue	76.7	high
Urinary bladder	tissue	75.8	high
Locus coeruleus	tissue	74.6
Choroid plexus	tissue	73.8
Cervix	tissue	72.8	medium
Skeletal muscle	tissue	66.2	not detected
Placenta	tissue	64.6	medium
Seminal vesicle	tissue	63.9	medium
Kidney	tissue	63.9	high
Postcentral gyrus	tissue	63.9
Esophagus	tissue	61.4	medium
Prefrontal cortex	tissue	60.2
Cerebral cortex	tissue	60.2	high
Occipital cortex	tissue	59.5
Hippocampal formation	tissue	59.3
Entorhinal cortex	tissue	58.7
Ovary	tissue	58.3	medium
Pancreas	tissue	57.1	medium
Motor cortex	tissue	55.8
Somatosensory cortex	tissue	55.5
Retrosplenial and cingulate cortex	tissue	52.8
Temporal cortex	tissue	51.4
Substantia nigra	tissue	51.0
Nucleus accumbens	tissue	49.9
Insular cortex	tissue	48.9
Retrosplenial cortex	tissue	48.7
Smooth muscle	tissue	47.9	not detected
Prostate	tissue	47.6	medium
Midbrain	tissue	47.2
Periaqueductal gray	tissue	46.9
Amygdala	tissue	46.3
Hippocampus	tissue	46.3	high
Vagina	tissue	46.2	high
Medulla oblongata	tissue	46.0
Hypothalamus	tissue	45.6
Thalamus	tissue	44.9
Lung	tissue	44.8	low
Spinal cord	tissue	44.4
Pons	tissue	43.7
Superior colliculi	tissue	40.9
Thyroid gland	tissue	40.1	medium
Pituitary gland	tissue	39.6
Parathyroid gland	tissue	39.4	medium
Septum	tissue	39.2
Thymus	tissue	38.0
Spleen	tissue	36.7	low
Corpus callosum	tissue	35.3
Adipose tissue	tissue	35.2	not detected
Endometrium 1	tissue	35.1	not detected
Appendix	tissue	35.1	high
Tongue	tissue	33.8

Brain sub-regions (HPA Brain Atlas): detected in 190; highest nTPM — Temporo-occipital transitional zone (81.9), Periaquaductal grey, lateral (76.5), Parieto-temporal junction (white matter) (74.7), Orbitofrontal gyrus, anterior (73.8), Cervical spinal cord, dorsal horn (73.0).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting SPATS2L by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 157 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 0.00579, LOEUF 0.722, missense Z 1.09 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000409140 splits into 3 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
2:200,389,245–200,439,328	227 / 257.4	0.88	no
2:200,440,649–200,469,993	104 / 162.5	0.64	no
2:200,469,994–200,478,028	284 / 280.1	1.01	no

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)

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
KCTD18	protein-coding	130535
SGO2	protein-coding	151246
TYW5	protein-coding	129450
MAIP1	protein-coding	79568
C2orf69	protein-coding	205327
AOX1	protein-coding	316
LINC01792	ncRNA	100507140

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

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUQ6-F1	63.72	0.34

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; nucleoli

Antibody reliability (HPA): IH uncertain · IF enhanced

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)

Type	Positions
N-acetylalanine	2
Phosphoserine	120, 455

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

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

GO Cellular Component (4): nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), protein-containing complex (GO:0032991)

GO top-level categories

8 GO namespaces:

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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 6 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO term	NS	Evidence
cytosol	CC	direct assay
nucleolus	CC	direct assay
protein-containing complex	CC	direct assay
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 763 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATS2L	RTP4	Q96DX8	618
SPATS2L	EPSTI1	Q96J88	611
SPATS2L	DNAJC6	O75061	488
SPATS2L	KCTD18	Q6PI47	479
SPATS2L	RSBN1L	Q6PCB5	477
SPATS2L	CYRIA	Q9H0Q0	442
SPATS2L	SLC22A15	Q8IZD6	438
SPATS2L	TMEM51	Q9NW97	433
SPATS2L	LRATD1	Q96KN4	428
SPATS2L	INTS13	Q9NVM9	427
SPATS2L	GLCCI1	Q86VQ1	425
SPATS2L	IFI6	P09912	423
SPATS2L	AKNAD1	Q5T1N1	401
SPATS2L	IFI44	Q8TCB0	399
SPATS2L	FBXO39	Q8N4B4	396

IntAct

Human interaction partners of SPATS2L in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

3 partners by confidence:

Partner	Interaction type	MIscore	Records
AP2A1	physical association	0.400	1
CUX1	association	0.350	1
FMR1	physical association	0.000	1

BioGRID (169 interactions; top human partners by supporting records): FGL1 (Affinity Capture-MS; 3 records), LTBR (Affinity Capture-MS; 3 records), FBL (Proximity Label-MS; 2 records), IFI16 (Affinity Capture-MS; 2 records), LRRC59 (Affinity Capture-MS; 2 records), MYC (Affinity Capture-MS; 2 records), SQSTM1 (Proximity Label-MS; 2 records), STK4 (Affinity Capture-MS; 2 records), TRIM44 (Affinity Capture-MS; 2 records), ACTG1 (Affinity Capture-MS), ADARB1 (Affinity Capture-MS), AKR7L (Affinity Capture-MS), ANAPC15 (Affinity Capture-MS), ANLN (Affinity Capture-MS), AP2M1 (Cross-Linking-MS (XL-MS))

Disease & clinical

Genetic variants

Variant evidence for SPATS2L: 104 ClinVar records (0 pathogenic / likely pathogenic); 75 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	85
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 38 predictions of 1,441):

Position(s)	Effect	Δscore	Sites
2:200306923	donor_loss	1.0000
2:200329429–200329430	acceptor_loss	1.0000	6
2:200383850	acceptor_gain	1.0000
2:200389220–200389222	acceptor_loss	1.0000	7
2:200389284–200389285	donor_loss	1.0000	5
2:200412309–200412310	acceptor_loss	1.0000	6
2:200419244	acceptor_gain	1.0000
2:200419248–200419249	acceptor_loss	1.0000	5
2:200419497–200419498	donor_loss	1.0000	5
2:200436204	donor_gain	1.0000

AlphaMissense

1,226 missense substitutions predicted likely pathogenic (of 3,690 scored), across 253 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M306	9	0.934	0.996
D328	8	0.999	1.000
D227	8	0.998	1.000
F47	8	0.991	1.000
F321	8	0.991	1.000
F257	8	0.987	0.999
F337	8	0.972	0.999
S25	8	0.960	0.998
D37	8	0.948	0.997
N26	8	0.938	0.989
D49	8	0.937	0.995
S323	8	0.937	0.999
D276	8	0.927	0.987
D247	8	0.911	0.990
D266	8	0.906	0.980
H320	8	0.904	0.995
D41	8	0.881	0.977
H356	8	0.823	0.971
W59	7	0.999	1.000
F36	7	0.996	0.999

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

4 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	7.26e-06
Uterine Corpus Endometrial Carcinoma (TCGA)	unfavorable	2.86e-05
Lung Adenocarcinoma (validation)	unfavorable	0.000495
Pancreatic Adenocarcinoma (TCGA)	unfavorable	0.000742

Disease associations

OMIM: gene MIM:613817 | disease phenotypes:

GWAS associations

showing 30 of 75 associations:

Study	Trait	p-value
GCST006414_103	Atrial fibrillation	6e-24
GCST006061_85	Atrial fibrillation	2e-20
GCST010796_775	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-20
GCST010796_769	Electrocardiogram morphology (amplitude at temporal datapoints)	3e-20
GCST010796_771	Electrocardiogram morphology (amplitude at temporal datapoints)	1e-19
GCST010796_768	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-19
GCST010796_772	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-19
GCST010796_770	Electrocardiogram morphology (amplitude at temporal datapoints)	6e-19
GCST010796_765	Electrocardiogram morphology (amplitude at temporal datapoints)	8e-19
GCST010796_766	Electrocardiogram morphology (amplitude at temporal datapoints)	8e-19
GCST010796_773	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-17
GCST006061_86	Atrial fibrillation	4e-17
GCST006803_100	Schizophrenia	4e-17
GCST010796_767	Electrocardiogram morphology (amplitude at temporal datapoints)	8e-17
GCST010796_764	Electrocardiogram morphology (amplitude at temporal datapoints)	9e-17
GCST010796_760	Electrocardiogram morphology (amplitude at temporal datapoints)	1e-16
GCST010796_759	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-16
GCST010796_761	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-16
GCST010796_762	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-16
GCST010796_752	Electrocardiogram morphology (amplitude at temporal datapoints)	3e-16
GCST010796_753	Electrocardiogram morphology (amplitude at temporal datapoints)	3e-16
GCST010796_754	Electrocardiogram morphology (amplitude at temporal datapoints)	5e-16
GCST010796_758	Electrocardiogram morphology (amplitude at temporal datapoints)	7e-16
GCST010796_755	Electrocardiogram morphology (amplitude at temporal datapoints)	1e-15
GCST010796_763	Electrocardiogram morphology (amplitude at temporal datapoints)	1e-15
GCST010796_751	Electrocardiogram morphology (amplitude at temporal datapoints)	1e-14
GCST010796_756	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-14
GCST010796_898	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-14
GCST010796_900	Electrocardiogram morphology (amplitude at temporal datapoints)	2e-14
GCST010796_899	Electrocardiogram morphology (amplitude at temporal datapoints)	3e-14

EFO canonical traits (from GWAS)

12 canonical traits:

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 (CPIC guideline: no)

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 abundance, increases expression, decreases expression, decreases reaction, affects cotreatment	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	increases expression, affects cotreatment, decreases expression	2
Acetaminophen	increases expression	2
Vehicle Emissions	decreases expression, decreases reaction, increases abundance, increases expression	2
Benzo(a)pyrene	increases methylation, affects methylation, decreases expression	2
Phenylmercuric Acetate	increases expression, affects cotreatment	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	affects binding, increases activity, increases expression	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	decreases ADP-ribosylation, increases ADP-ribosylation	1
CGP 52608	increases reaction, affects binding	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression, decreases reaction	1
dorsomorphin	increases expression, affects cotreatment	1
LDN 193189	affects cotreatment, decreases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	decreases expression, affects cotreatment	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)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for SPATS2L across ~30M SureChEMBL compounds — explore on Sugi Predict.