SPACA5

Summary

SPACA5 (sperm acrosome associated 5, HGNC:31353) is a protein-coding gene on chromosome Xp11.23, encoding Sperm acrosome-associated protein 5 (Q96QH8).

Predicted to enable lysozyme activity. Predicted to be involved in fusion of sperm to egg plasma membrane involved in single fertilization. Predicted to be located in extracellular region. Predicted to be active in acrosomal vesicle and sperm flagellum.

Source: NCBI Gene 389852 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 9 total
• MANE Select transcript: NM_001394298

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31353
Approved symbol	SPACA5
Name	sperm acrosome associated 5
Location	Xp11.23
Locus type	gene with protein product
Status	Approved
Aliases	SLLP2, LYZL5, LYC5, UNQ6288, dJ54B20.3, PNPK6288
Ensembl gene	ENSG00000171489
Ensembl biotype	protein_coding
OMIM	300593
Entrez	389852

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000304355, ENST00000376940

RefSeq mRNA: 2 — MANE Select: NM_001394298 NM_001394298, NM_205856

CCDS: CCDS14286

Canonical transcript exons

ENST00000376940 — 4 exons

Exon	Start	End
ENSE00001152610	48006988	48007947
ENSE00001625722	48009366	48009444
ENSE00001696801	48009549	48009733
ENSE00001768442	48008376	48008534

Expression profiles

Bgee: expression breadth ubiquitous, 122 present calls, max score 96.24.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.59	gold quality
left testis	UBERON:0004533	74.46	gold quality
testis	UBERON:0000473	74.06	gold quality
right testis	UBERON:0004534	73.34	gold quality
corpus callosum	UBERON:0002336	54.47	gold quality
right uterine tube	UBERON:0001302	53.11	gold quality
endometrium	UBERON:0001295	52.56	gold quality
mucosa of transverse colon	UBERON:0004991	51.43	gold quality
sural nerve	UBERON:0015488	49.72	silver quality
lymph node	UBERON:0000029	49.45	gold quality
body of pancreas	UBERON:0001150	48.97	gold quality
cerebellar cortex	UBERON:0002129	48.86	gold quality
cerebellar hemisphere	UBERON:0002245	48.86	gold quality
cerebellum	UBERON:0002037	48.61	gold quality
colonic epithelium	UBERON:0000397	48.24	gold quality
left lobe of thyroid gland	UBERON:0001120	48.19	gold quality
thyroid gland	UBERON:0002046	48.17	gold quality
right lobe of thyroid gland	UBERON:0001119	48.06	gold quality
right hemisphere of cerebellum	UBERON:0014890	47.68	gold quality
putamen	UBERON:0001874	47.50	gold quality
left uterine tube	UBERON:0001303	46.83	gold quality
rectum	UBERON:0001052	46.47	gold quality
nucleus accumbens	UBERON:0001882	46.46	gold quality
fallopian tube	UBERON:0003889	46.41	gold quality
caudate nucleus	UBERON:0001873	46.20	gold quality
left ovary	UBERON:0002119	45.88	gold quality
hypothalamus	UBERON:0001898	45.68	gold quality
body of uterus	UBERON:0009853	45.60	gold quality
muscle layer of sigmoid colon	UBERON:0035805	45.56	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.22

Regulation

Is transcription factor: no

Cross-species orthologs

14 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spaca5	ENSMUSG00000037167
rattus_norvegicus	Spaca5	ENSRNOG00000045622
drosophila_melanogaster	LysB	FBGN0004425
drosophila_melanogaster	LysD	FBGN0004427
drosophila_melanogaster	LysE	FBGN0004428
drosophila_melanogaster	LysP	FBGN0004429
drosophila_melanogaster	LysS	FBGN0004430
drosophila_melanogaster	LysX	FBGN0004431
drosophila_melanogaster	CG16756	FBGN0029765
drosophila_melanogaster	CG7798	FBGN0034092
drosophila_melanogaster	CG16799	FBGN0034538
drosophila_melanogaster	CG11159	FBGN0034539
drosophila_melanogaster	CG8492	FBGN0035813
drosophila_melanogaster	CG30062	FBGN0050062

Paralogs (8): LYZ (ENSG00000090382), LYZL1 (ENSG00000120563), SPACA3 (ENSG00000141316), LYZL2 (ENSG00000151033), LYZL4 (ENSG00000157093), LALBA (ENSG00000167531), SPACA5B (ENSG00000171478), LYZL6 (ENSG00000275722)

Protein

Protein identifiers

Sperm acrosome-associated protein 5 — Q96QH8 (reviewed: Q96QH8)

Alternative names: Lysozyme-like protein 5, Sperm-specific lysozyme-like protein X

All UniProt accessions (2): Q96QH8, A0A140VJN7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the glycosyl hydrolase 22 family.

RefSeq proteins (2): NP_001381227, NP_995328 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000974	Glyco_hydro_22_lys	Family
IPR001916	Glyco_hydro_22	Family
IPR023346	Lysozyme-like_dom_sf	Homologous_superfamily

Pfam: PF00062

UniProt features (9 total): disulfide bond 4, signal peptide 1, chain 1, domain 1, active site 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96QH8-F1	91.04	0.80

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 56

Disulfide bonds (4): 27–147, 51–135, 85–100, 96–114

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 32 (showing top): GOBP_SINGLE_FERTILIZATION, GOCC_SECRETORY_GRANULE, GOBP_MEMBRANE_FUSION, GOBP_PLASMA_MEMBRANE_ORGANIZATION, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_PLASMA_MEMBRANE_FUSION, GOBP_MEMBRANE_ORGANIZATION, GOBP_FERTILIZATION, GOCC_SECRETORY_VESICLE, GOCC_MOTILE_CILIUM, GOCC_ACROSOMAL_VESICLE, GOCC_CILIUM, GOMF_LYSOZYME_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_GLYCOSYL_BONDS

GO Biological Process (1): fusion of sperm to egg plasma membrane involved in single fertilization (GO:0007342)

GO Molecular Function (3): lysozyme activity (GO:0003796), hydrolase activity (GO:0016787), hydrolase activity, acting on glycosyl bonds (GO:0016798)

GO Cellular Component (3): acrosomal vesicle (GO:0001669), extracellular region (GO:0005576), sperm flagellum (GO:0036126)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
single fertilization	1
cellular process involved in reproduction in multicellular organism	1
hydrolase activity, hydrolyzing O-glycosyl compounds	1
peptidoglycan muralytic activity	1
catalytic activity	1
hydrolase activity	1
secretory granule	1
cellular anatomical structure	1
9+2 motile cilium	1

Protein interactions and networks

STRING

378 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPACA5	ZNF630	Q2M218	627
SPACA5	ZNF212	Q9UDV6	472
SPACA5	CYLC1	P35663	468
SPACA5	TMEM190	Q8WZ59	452
SPACA5	ZNF182	P17025	446
SPACA5	ZNF81	P51508	418
SPACA5	CIMAP1A	Q96PU9	380
SPACA5	IZUMO4	Q1ZYL8	376
SPACA5	AKAP14	Q86UN6	374
SPACA5	TCP11	Q8WWU5	371
SPACA5	C12orf71	A8MTZ7	363
SPACA5	ODF4	Q2M2E3	362
SPACA5	ASTL	Q6HA08	358
SPACA5	EOLA1	Q8TE69	358
SPACA5	IZUMO2	Q6UXV1	354

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A2AE20, C0HLB7, C1IIX1, D4ABW7, D9J142, D9J143, G3XDT7, O75951, P00702, P00709, P00710, P00711, P00712, P00713, P00714, P00716, P05105, P07458, P08334, P08896, P09462, P11375, P11376, P12065, P18137, P28546, P29752, P30805, P37161, P48816, P50717, P50718, P51782, P61944, P81646, P81708, P85045, Q06655, Q29145, Q29RT1

Diamond homologs: A0JNM6, A2AE20, A6QQ77, B6VH75, B6VH76, G3XDT7, O75951, P00697, P00698, P00699, P00700, P00701, P00702, P00703, P00704, P00705, P00706, P00707, P00708, P04421, P08905, P11375, P11376, P11941, P12066, P12067, P12068, P12069, P16973, P17607, P17897, P19849, P22910, P24364, P24533, P30201, P37712, P37713, P49663, P61626

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

508 predictions. Top by Δscore:

Variant	Effect	Δscore
X:48008532:ATGG:A	donor_loss	1.0000
X:48008534:GGT:G	donor_loss	1.0000
X:48008535:G:C	donor_loss	1.0000
X:48008536:T:A	donor_loss	1.0000
X:48008375:GGGCT:G	acceptor_gain	0.9900
X:48008530:TCATG:T	donor_gain	0.9900
X:48008533:TG:T	donor_gain	0.9900
X:48008534:GG:G	donor_gain	0.9900
X:48008535:G:GG	donor_gain	0.9900
X:48009362:TCA:T	acceptor_loss	0.9900
X:48009364:A:AG	acceptor_gain	0.9900
X:48009364:AGAC:A	acceptor_loss	0.9900
X:48009365:G:GA	acceptor_gain	0.9900
X:48009365:GAC:G	acceptor_gain	0.9900
X:48009365:GACCT:G	acceptor_gain	0.9900
X:48008370:CCCCA:C	acceptor_loss	0.9800
X:48008371:CCCAG:C	acceptor_loss	0.9800
X:48008372:CCAGG:C	acceptor_loss	0.9800
X:48008373:CAG:C	acceptor_loss	0.9800
X:48008531:CATG:C	donor_gain	0.9800
X:48008374:A:AG	acceptor_gain	0.9700
X:48008375:G:GG	acceptor_gain	0.9700
X:48008532:ATG:A	donor_gain	0.9700
X:48009365:GA:G	acceptor_gain	0.9700
X:48009440:GCCTG:G	donor_gain	0.9700
X:48007944:GACT:G	donor_gain	0.9600
X:48008374:AG:A	acceptor_gain	0.9600
X:48008375:GG:G	acceptor_gain	0.9600
X:48009365:GACC:G	acceptor_gain	0.9600
X:48009441:CCTGG:C	donor_loss	0.9600

AlphaMissense

1059 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003688664 (X:48003454 C>T), RS1003762069 (X:48002949 G>A), RS1008275863 (X:48003921 A>C), RS1008329662 (X:48004110 G>A), RS1012499880 (X:48003464 G>A), RS1012923080 (X:48003807 C>T), RS1014553217 (X:48004162 C>A,T), RS1017744248 (X:48002439 C>T), RS1018335777 (X:48004119 C>G,T), RS1022288750 (X:48003009 T>A), RS1022723293 (X:48003481 C>T), RS1026442669 (X:48002897 G>A,C), RS1027892258 (X:48004145 C>A,T), RS1030996294 (X:48003894 C>T), RS1038679193 (X:48002830 T>C)

Disease associations

OMIM: gene MIM:300593 | 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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
mono-(2-ethylhexyl)phthalate	decreases expression	1
butylbenzyl phthalate	increases expression	1
Benzo(a)pyrene	affects methylation	1
Aflatoxin B1	decreases methylation	1
Permethrin	increases expression	1

Clinical trials (associated diseases)

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