SPATA2L

Summary

SPATA2L (spermatogenesis associated 2 like, HGNC:28393) is a protein-coding gene on chromosome 16q24.3, encoding Spermatogenesis-associated protein 2-like protein (Q8IUW3).

Predicted to be active in cytoplasm.

Source: NCBI Gene 124044 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_152339

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28393
Approved symbol	SPATA2L
Name	spermatogenesis associated 2 like
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC26885, tamo
Ensembl gene	ENSG00000158792
Ensembl biotype	protein_coding
Entrez	124044

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000289805, ENST00000335360, ENST00000569918, ENST00000852052, ENST00000852053, ENST00000928087

RefSeq mRNA: 1 — MANE Select: NM_152339 NM_152339

CCDS: CCDS10985

Canonical transcript exons

ENST00000289805 — 3 exons

Exon	Start	End
ENSE00001041032	89700930	89701233
ENSE00001308952	89701628	89701705
ENSE00001377246	89696357	89698305

Expression profiles

Bgee: expression breadth ubiquitous, 269 present calls, max score 97.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.4379 / max 74.3740, expressed in 1573 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158645	2.9300	1409
158644	0.8407	419
158642	0.3691	168
158643	0.2981	129

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	97.56	gold quality
cervix squamous epithelium	UBERON:0006922	94.37	gold quality
CA1 field of hippocampus	UBERON:0003881	91.07	gold quality
nephron tubule	UBERON:0001231	90.10	gold quality
parotid gland	UBERON:0001831	88.25	gold quality
lower lobe of lung	UBERON:0008949	87.79	gold quality
jejunal mucosa	UBERON:0000399	87.63	gold quality
tendon of biceps brachii	UBERON:0008188	87.45	gold quality
endothelial cell	CL:0000115	87.17	silver quality
colonic mucosa	UBERON:0000317	87.09	gold quality
metanephric glomerulus	UBERON:0004736	86.46	gold quality
kidney epithelium	UBERON:0004819	86.31	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.30	gold quality
mammary duct	UBERON:0001765	86.06	silver quality
mucosa of urinary bladder	UBERON:0001259	85.96	gold quality
renal glomerulus	UBERON:0000074	85.89	gold quality
Brodmann (1909) area 46	UBERON:0006483	85.47	gold quality
buccal mucosa cell	CL:0002336	85.17	gold quality
epithelium of mammary gland	UBERON:0003244	85.14	silver quality
blood	UBERON:0000178	85.05	gold quality
entorhinal cortex	UBERON:0002728	84.65	gold quality
hair follicle	UBERON:0002073	84.38	silver quality
amniotic fluid	UBERON:0000173	83.91	gold quality
mucosa of transverse colon	UBERON:0004991	83.73	gold quality
mucosa of paranasal sinus	UBERON:0005030	83.53	silver quality
adult organism	UBERON:0007023	83.29	gold quality
metanephros	UBERON:0000081	83.12	gold quality
gingiva	UBERON:0001828	82.36	silver quality
pituitary gland	UBERON:0000007	82.32	gold quality
cauda epididymis	UBERON:0004360	82.32	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting SPATA2L, 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-23B-5P	99.98	66.07	587
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-92A-2-5P	99.75	67.01	2164
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-4297	98.77	66.95	2013
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-3180	98.46	64.68	348
HSA-MIR-3180-3P	98.46	64.68	348
HSA-MIR-6816-5P	98.46	64.35	364
HSA-MIR-5691	98.23	67.02	1335
HSA-MIR-6805-3P	98.23	67.02	1334
HSA-MIR-4518	98.12	66.82	1030
HSA-MIR-5581-5P	97.91	66.50	965
HSA-MIR-6893-3P	97.79	64.91	1238
HSA-MIR-8089	97.74	66.21	1698
HSA-MIR-1266-5P	97.71	66.92	1052
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-1226-3P	97.51	66.32	1063
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-509-3-5P	97.21	67.74	1517

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	spata2l	ENSDARG00000068814
mus_musculus	Spata2l	ENSMUSG00000033594
rattus_norvegicus	Spata2L	ENSRNOG00000016167
drosophila_melanogaster	tamo	FBGN0041582

Paralogs (1): SPATA2 (ENSG00000158480)

Protein

Protein identifiers

Spermatogenesis-associated protein 2-like protein — Q8IUW3 (reviewed: Q8IUW3)

All UniProt accessions (2): Q8IUW3, H3BVE5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the SPATA2 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8IUW3-1	1	yes
Q8IUW3-2	2

RefSeq proteins (1): NP_689552* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR048839	SPATA2_PUB-like	Domain

Pfam: PF21388

UniProt features (6 total): region of interest 2, splice variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IUW3-F1	72.64	0.49

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): 327

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): RNGTGGGC_UNKNOWN, NAGASHIMA_NRG1_SIGNALING_UP, USF_C, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, OSMAN_BLADDER_CANCER_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, ARNT_01, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, OHGUCHI_LIVER_HNF4A_TARGETS_DN, KRIEG_HYPOXIA_NOT_VIA_KDM3A, IL2_UP.V1_UP, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP, RBM34_TARGET_GENES, RYBP_TARGET_GENES, MIR498_3P

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA2L	CYLD	Q9NQC7	482
SPATA2L	DBNDD1	Q9H9R9	479
SPATA2L	DEF8	Q6ZN54	447
SPATA2L	ABHD8	Q96I13	432
SPATA2L	CENPBD1P	B2RD01	431
SPATA2L	SPATA33	Q96N06	430
SPATA2L	CPNE7	Q9UBL6	406
SPATA2L	PGBD4	Q96DM1	380
SPATA2L	ZMYND19	Q96E35	377
SPATA2L	CDK10	Q15131	367
SPATA2L	MYO15B	Q96JP2	360
SPATA2L	TMEM168	Q9H0V1	359
SPATA2L	SMIM30	A4D0T7	350
SPATA2L	DHRS7B	Q6IAN0	349
SPATA2L	TTC14	Q96N46	348
SPATA2L	SPG7	Q9UQ90	348

IntAct

78 interactions, top by confidence:

A	B	Type	Score
GRB2	SPATA2L	psi-mi:“MI:0915”(physical association)	0.740
GRB2	WIPF3	psi-mi:“MI:0914”(association)	0.730
NCK2	SPATA2L	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	APBB2	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	APOE	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	APP	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	DBH	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L		psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	ELAVL4	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	GFAP	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	NDUFV2	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	NOS3	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	PRKN	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	PECAM1	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	NDRG1	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	PARK7	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	ATXN10	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	TDP1	psi-mi:“MI:0915”(physical association)	0.560
SPATA2L	JPH3	psi-mi:“MI:0915”(physical association)	0.560
HTT	SPATA2L	psi-mi:“MI:0915”(physical association)	0.560
ATXN3	SPATA2L	psi-mi:“MI:0915”(physical association)	0.560
ATXN1	SPATA2L	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (21): SPATA2L (Proximity Label-MS), SPATA2L (Proximity Label-MS), SPATA2L (Affinity Capture-MS), SPATA2L (Affinity Capture-MS), SPATA2L (Affinity Capture-MS), SPATA2L (Affinity Capture-RNA), SPATA2L (Affinity Capture-MS), SPATA2L (Two-hybrid), GRB2 (Two-hybrid), SPATA2L (Proximity Label-MS), SPATA2L (Two-hybrid), DCAF10 (Affinity Capture-MS), SPATA2L (Affinity Capture-MS), PAGE5 (Affinity Capture-MS), SPATA2L (Affinity Capture-Western)

ESM2 similar proteins: A0A8I5KY20, A2A9T0, A2IDD5, B0BNK9, B8ZZ34, C9JI98, C9JLR9, F5GYI3, O18734, P0CG25, P84157, Q0IIA6, Q0PHV7, Q0X0E2, Q13387, Q1RMK9, Q2M3D2, Q2TAM9, Q3ZCQ3, Q4VA45, Q673H1, Q69YZ2, Q6NS60, Q6P6N5, Q6PJ61, Q7Z6J2, Q80ZJ8, Q810I0, Q86SX3, Q86UD0, Q86XT2, Q8BNN1, Q8IUW3, Q8N4Y2, Q8N6N2, Q8QZV0, Q8R4T5, Q8TF61, Q8VCR9, Q8WXF8

Diamond homologs: F1QCY8, Q0IIA6, Q66HP6, Q8BNN1, Q8IUW3, Q8K004, Q9UM82, Q9W1A4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 34 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.

GO biological processes:

GO term	Partners	Fold	FDR
learning	5	43.9×	6e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

504 predictions. Top by Δscore:

Variant	Effect	Δscore
16:89698301:AAGGT:A	acceptor_gain	1.0000
16:89698302:AGGT:A	acceptor_gain	1.0000
16:89698303:GGT:G	acceptor_gain	1.0000
16:89698304:GT:G	acceptor_gain	1.0000
16:89698304:GTC:G	acceptor_loss	1.0000
16:89698305:TCTG:T	acceptor_loss	1.0000
16:89698306:C:CC	acceptor_gain	1.0000
16:89700924:GCCTA:G	donor_loss	1.0000
16:89700925:CCTAC:C	donor_loss	1.0000
16:89700926:CTAC:C	donor_loss	1.0000
16:89700927:TA:T	donor_loss	1.0000
16:89700928:A:AT	donor_loss	1.0000
16:89700929:C:A	donor_loss	1.0000
16:89701232:TC:T	acceptor_gain	1.0000
16:89701233:CC:C	acceptor_gain	1.0000
16:89700950:T:TA	donor_gain	0.9900
16:89701229:CCATC:C	acceptor_gain	0.9900
16:89701230:CATC:C	acceptor_gain	0.9900
16:89701230:CATCC:C	acceptor_gain	0.9900
16:89701232:TCC:T	acceptor_loss	0.9900
16:89701233:CCTG:C	acceptor_loss	0.9900
16:89701234:C:A	acceptor_loss	0.9900
16:89701234:C:CC	acceptor_gain	0.9900
16:89701235:T:G	acceptor_loss	0.9900
16:89701240:C:CT	acceptor_gain	0.9900
16:89698309:C:CT	acceptor_gain	0.9800
16:89700928:A:AC	donor_gain	0.9800
16:89700929:C:CC	donor_gain	0.9800
16:89701231:ATC:A	acceptor_gain	0.9800
16:89701238:G:T	acceptor_gain	0.9800

AlphaMissense

2665 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:89698300:G:C	F103L	0.999
16:89698300:G:T	F103L	0.999
16:89698302:A:G	F103L	0.999
16:89700951:C:A	R94S	0.998
16:89700951:C:G	R94S	0.998
16:89700952:C:A	R94M	0.998
16:89700952:C:G	R94T	0.998
16:89700956:A:G	W93R	0.998
16:89700956:A:T	W93R	0.998
16:89700934:A:T	I100N	0.997
16:89700942:G:C	F97L	0.997
16:89700942:G:T	F97L	0.997
16:89700943:A:G	F97S	0.997
16:89700944:A:G	F97L	0.997
16:89700954:C:A	W93C	0.997
16:89700954:C:G	W93C	0.997
16:89700988:T:A	E82V	0.997
16:89700989:C:T	E82K	0.997
16:89700934:A:C	I100S	0.996
16:89698238:A:G	F124S	0.995
16:89698295:C:T	G105E	0.995
16:89700979:G:T	A85E	0.995
16:89700980:C:G	A85P	0.995
16:89698154:G:T	A152D	0.994
16:89698227:C:G	G128R	0.994
16:89698290:A:C	Y107D	0.994
16:89700934:A:G	I100T	0.994
16:89700987:C:A	E82D	0.994
16:89700987:C:G	E82D	0.994
16:89698224:A:G	Y129H	0.993

dbSNP variants (sampled 300 via entrez): RS1000544928 (16:89702512 T>A), RS1000602073 (16:89702971 G>C), RS1000616039 (16:89698936 C>A,T), RS1000909763 (16:89702742 G>A,C), RS1001016784 (16:89700793 C>A,G,T), RS1001281739 (16:89701346 G>A,T), RS1001291191 (16:89696914 G>A,C), RS1001363097 (16:89696790 A>G,T), RS1001585813 (16:89701118 G>A,C,T), RS1002185330 (16:89701976 C>A,G), RS1002654706 (16:89703239 G>A), RS1002853302 (16:89700250 G>A), RS1003844636 (16:89696063 G>C,T), RS1003916686 (16:89695928 G>T), RS1004053015 (16:89699548 G>A,C)

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

5 associations (top):

Study	Trait	p-value
GCST004602_287	Mean corpuscular volume	7.000000e-14
GCST006988_146	Blond vs. brown/black hair color	8.000000e-23
GCST007876_65	Estimated glomerular filtration rate	3.000000e-08
GCST010083_322	Hemoglobin levels	3.000000e-22
GCST010703_280	Brain morphology (MOSTest)	2.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003924	hair color
EFO:0004509	hemoglobin measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression	2
Valproic Acid	affects expression, increases expression	2
urushiol	decreases expression	1
triphenyl phosphate	affects expression	1
ferrous chloride	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
licochalcone B	increases expression	1
PCI 5002	affects cotreatment, increases expression	1
Air Pollutants	affects expression, increases abundance	1
Amiodarone	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	decreases expression	1
Coumestrol	decreases expression	1
Diazinon	increases methylation	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Zinc	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Okadaic Acid	increases expression	1
Genistein	decreases expression	1

Clinical trials (associated diseases)

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