SPATA1

Summary

SPATA1 (spermatogenesis associated 1, HGNC:14682) is a protein-coding gene on chromosome 1p22.3, encoding Spermatogenesis-associated protein 1 (Q5VX52).

Predicted to be located in acrosomal vesicle.

Source: NCBI Gene 100505741 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001397487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14682
Approved symbol	SPATA1
Name	spermatogenesis associated 1
Location	1p22.3
Locus type	gene with protein product
Status	Approved
Aliases	SP-2
Ensembl gene	ENSG00000122432
Ensembl biotype	protein_coding
Entrez	100505741

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding_CDS_not_defined, 3 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding

ENST00000460286, ENST00000468437, ENST00000473108, ENST00000484939, ENST00000485121, ENST00000490879, ENST00000697276, ENST00000697277, ENST00000699394, ENST00000699524

RefSeq mRNA: 2 — MANE Select: NM_001397487 NM_001310156, NM_001397487

CCDS: CCDS90993

Canonical transcript exons

ENST00000699524 — 14 exons

Exon	Start	End
ENSE00002170571	84506386	84506418
ENSE00002448040	84525845	84526073
ENSE00003537063	84516223	84516395
ENSE00003810946	84525696	84525749
ENSE00003976844	84545634	84545759
ENSE00003976845	84555910	84555979
ENSE00003976847	84532860	84532974
ENSE00003976849	84565861	84567379
ENSE00003976850	84520585	84520691
ENSE00003976851	84548786	84548964
ENSE00003976852	84544202	84544304
ENSE00003976853	84522390	84522507
ENSE00003976854	84533709	84533766
ENSE00003976855	84550432	84550530

Expression profiles

Bgee: expression breadth ubiquitous, 176 present calls, max score 91.23.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1998 / max 11.4203, expressed in 68 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
3800	0.1998	68

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	91.23	silver quality
sperm	CL:0000019	89.65	gold quality
male germ cell	CL:0000015	86.26	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.49	gold quality
left testis	UBERON:0004533	79.05	gold quality
right testis	UBERON:0004534	78.37	gold quality
testis	UBERON:0000473	77.56	gold quality
monocyte	CL:0000576	77.20	gold quality
mononuclear cell	CL:0000842	76.95	gold quality
calcaneal tendon	UBERON:0003701	76.80	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.24	gold quality
leukocyte	CL:0000738	76.03	gold quality
granulocyte	CL:0000094	75.51	gold quality
right lobe of liver	UBERON:0001114	75.51	gold quality
lower esophagus mucosa	UBERON:0035834	75.18	gold quality
apex of heart	UBERON:0002098	73.92	gold quality
adenohypophysis	UBERON:0002196	73.74	gold quality
spleen	UBERON:0002106	73.01	gold quality
tendon	UBERON:0000043	72.45	gold quality
metanephros cortex	UBERON:0010533	72.11	gold quality
mucosa of stomach	UBERON:0001199	71.98	gold quality
mucosa of transverse colon	UBERON:0004991	71.90	gold quality
right lung	UBERON:0002167	71.38	gold quality
descending thoracic aorta	UBERON:0002345	71.36	gold quality
body of uterus	UBERON:0009853	71.18	gold quality
thoracic aorta	UBERON:0001515	70.98	gold quality
right coronary artery	UBERON:0001625	70.97	gold quality
ascending aorta	UBERON:0001496	70.95	gold quality
muscle layer of sigmoid colon	UBERON:0035805	70.77	gold quality
transverse colon	UBERON:0001157	70.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.23

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	SPATA1	ENSDARG00000094327
mus_musculus	Spata1	ENSMUSG00000028188
rattus_norvegicus	Spata1	ENSRNOG00000015678

Protein

Protein identifiers

Spermatogenesis-associated protein 1 — Q5VX52 (reviewed: Q5VX52)

Alternative names: Sperm-specific protein SP-2

All UniProt accessions (4): A0A8V8TNC2, A0A8V8TNU4, A0A8V8TPQ3, A0A8V8TQ46

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with IFT20.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5VX52-1	1	yes
Q5VX52-2	2
Q5VX52-4	3

RefSeq proteins (2): NP_001297085, NP_001384416* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031478	SPATA1_C	Domain
IPR039062	SPAT1	Family

Pfam: PF15743

UniProt features (11 total): splice variant 3, sequence conflict 2, coiled-coil region 2, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VX52-F1	69.58	0.45

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): GOCC_SECRETORY_GRANULE, TCCAGAT_MIR5165P, chr1p22, GOCC_SECRETORY_VESICLE, GOCC_ACROSOMAL_VESICLE, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, IL15_UP.V1_DN, IL2_UP.V1_DN, HHEX_TARGET_GENES, NAB2_TARGET_GENES, NKX2_3_TARGET_GENES, PAF1_TARGET_GENES, UBN1_TARGET_GENES, ZNF22_TARGET_GENES, ZNF274_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): acrosomal vesicle (GO:0001669), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
secretory granule	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

204 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPATA1	SPATA6L	Q8N4H0	445
SPATA1	SPATA6	Q9NWH7	396
SPATA1	SPEF1	Q9Y4P9	370
SPATA1	CTBS	Q01459	367
SPATA1	SPATA20	Q8TB22	357
SPATA1	SPATA17	Q96L03	355
SPATA1	SPATA4	Q8NEY3	348
SPATA1	GMCL1	Q96IK5	338
SPATA1	SPATA7	Q9P0W8	317
SPATA1	SPAG16	Q8N0X2	305
SPATA1	SPATA22	Q8NHS9	302
SPATA1	SRM	P19623	289
SPATA1	LCA5	Q86VQ0	288
SPATA1	ETNPPL	Q8TBG4	272
SPATA1	GNG5	P30670	270

IntAct

2 interactions, top by confidence:

A	B	Type	Score
SPATA1	PCK1	psi-mi:“MI:0914”(association)	0.350

BioGRID (33): SPATA1 (Two-hybrid), UBR4 (Affinity Capture-MS), SCYL2 (Affinity Capture-MS), TLK2 (Affinity Capture-MS), TLK1 (Affinity Capture-MS), MAP3K4 (Affinity Capture-MS), WNK2 (Affinity Capture-MS), SMG6 (Affinity Capture-MS), WNK1 (Affinity Capture-MS), LRRC49 (Affinity Capture-MS), VPS39 (Affinity Capture-MS), C2orf44 (Affinity Capture-MS), NECAP2 (Affinity Capture-MS), KDM5C (Affinity Capture-MS), CMTR1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1W2P884, A2RUB6, A7E3D8, A8MT70, B0CM36, B2RYR0, F1PZQ5, O95447, Q0IIM1, Q0P5X1, Q2KHM9, Q2T9X8, Q4KLH6, Q4R3Q7, Q4R6Q9, Q5NVK0, Q5R7F8, Q5RBD6, Q5RBY6, Q5RC32, Q5RD75, Q5SZL2, Q5TB80, Q5TID7, Q5VX52, Q5XI03, Q6A000, Q6NS45, Q6NZK5, Q6ZPR1, Q6ZQ06, Q7Z4H7, Q80VP2, Q80XJ2, Q80ZU5, Q86T90, Q86YF9, Q8BMD2, Q8IYW5, Q8N0Z3

Diamond homologs: Q5VX52, Q6AY22, Q9D5R4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

554 predictions. Top by Δscore:

Variant	Effect	Δscore
1:84563243:A:AC	donor_gain	1.0000
1:84563244:C:CC	donor_gain	1.0000
1:84563255:A:AC	donor_gain	1.0000
1:84563256:C:CC	donor_gain	1.0000
1:84563414:TGATC:T	acceptor_gain	1.0000
1:84563419:C:A	acceptor_loss	1.0000
1:84563419:C:CC	acceptor_gain	1.0000
1:84563420:T:A	acceptor_loss	1.0000
1:84563729:TCCTA:T	donor_loss	1.0000
1:84563731:CTACC:C	donor_loss	1.0000
1:84563733:A:AT	donor_loss	1.0000
1:84564206:A:C	donor_gain	1.0000
1:84565835:TCTTA:T	donor_loss	1.0000
1:84565836:CTTA:C	donor_loss	1.0000
1:84565837:TTA:T	donor_loss	1.0000
1:84565838:TA:T	donor_loss	1.0000
1:84565839:A:AC	donor_gain	1.0000
1:84565840:C:A	donor_loss	1.0000
1:84565840:C:CC	donor_gain	1.0000
1:84555030:T:TA	donor_gain	0.9900
1:84555031:C:A	donor_gain	0.9900
1:84563417:TC:T	acceptor_gain	0.9900
1:84563418:CC:C	acceptor_gain	0.9900
1:84565834:GTCTT:G	donor_loss	0.9900
1:84565839:AC:A	donor_gain	0.9900
1:84565840:CC:C	donor_gain	0.9900
1:84565840:CCA:C	donor_gain	0.9900
1:84565840:CCAG:C	donor_gain	0.9900
1:84565884:TTCTG:T	donor_gain	0.9900
1:84566009:TTACC:T	acceptor_gain	0.9900

AlphaMissense

2860 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:84520610:T:A	V43D	0.996
1:84520624:T:A	W48R	0.996
1:84520624:T:C	W48R	0.996
1:84520601:T:A	V40D	0.995
1:84520626:G:C	W48C	0.994
1:84520626:G:T	W48C	0.994
1:84520684:T:C	F68L	0.994
1:84520686:T:A	F68L	0.994
1:84520686:T:G	F68L	0.994
1:84525861:T:C	L133S	0.994
1:84522476:T:C	F99S	0.992
1:84522479:T:C	L100P	0.992
1:84525735:T:C	F123L	0.992
1:84525737:T:A	F123L	0.992
1:84525737:T:G	F123L	0.992
1:84525867:T:C	L135S	0.992
1:84522469:T:C	F97L	0.991
1:84522471:T:A	F97L	0.991
1:84522471:T:G	F97L	0.991
1:84525863:T:G	Y134D	0.991
1:84522410:T:C	L77S	0.990
1:84522419:T:C	L80P	0.990
1:84522475:T:C	F99L	0.990
1:84522477:T:A	F99L	0.990
1:84522477:T:G	F99L	0.990
1:84525721:T:C	L118P	0.990
1:84520595:T:C	L38P	0.989
1:84522500:T:C	L107S	0.989
1:84520625:G:C	W48S	0.988
1:84520669:T:C	F63L	0.988

dbSNP variants (sampled 300 via entrez): RS1000019693 (1:84530081 C>T), RS1000087909 (1:84528671 T>A,C), RS1000090045 (1:84510811 C>T), RS1000130325 (1:84558552 A>G), RS1000185189 (1:84549896 C>A,T), RS1000222999 (1:84508936 G>C,T), RS1000251317 (1:84558259 C>G), RS1000278089 (1:84551503 A>C), RS1000289753 (1:84551792 T>C), RS1000296687 (1:84508591 T>G), RS1000300596 (1:84514606 G>A), RS1000307211 (1:84518046 T>C), RS1000396000 (1:84565154 G>A), RS1000441163 (1:84544897 A>C), RS1000497511 (1:84529796 T>G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
hydroxyhydroquinone	increases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression	1
maleic acid	increases expression	1
Doxorubicin	decreases expression	1
Urethane	increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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