SPACA7

Summary

SPACA7 (sperm acrosome associated 7, HGNC:29575) is a protein-coding gene on chromosome 13q34, encoding Sperm acrosome-associated protein 7 (Q96KW9). Involved in fertilization.

Predicted to act upstream of or within negative regulation of cell adhesion and single fertilization. Located in acrosomal vesicle.

Source: NCBI Gene 122258 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 31 total — 1 pathogenic
• MANE Select transcript: NM_145248

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29575
Approved symbol	SPACA7
Name	sperm acrosome associated 7
Location	13q34
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000153498
Ensembl biotype	protein_coding
Entrez	122258

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000283550, ENST00000375699, ENST00000414180, ENST00000443541

RefSeq mRNA: 1 — MANE Select: NM_145248 NM_145248

CCDS: CCDS9524

Canonical transcript exons

ENST00000283550 — 7 exons

Exon	Start	End
ENSE00001011097	112398049	112398138
ENSE00001011099	112432444	112432521
ENSE00001011101	112393021	112393077
ENSE00001011102	112401069	112401164
ENSE00001123970	112376355	112376479
ENSE00001192675	112434485	112434689
ENSE00003784844	112399066	112399173

Expression profiles

Bgee: expression breadth broad, 62 present calls, max score 95.91.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1664 / max 185.8470, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136146	0.1587	3
136145	0.0077	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.91	gold quality
right testis	UBERON:0004534	95.85	gold quality
testis	UBERON:0000473	95.24	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.54	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	64.85	silver quality
liver	UBERON:0002107	52.27	gold quality
right lobe of liver	UBERON:0001114	49.50	gold quality
right uterine tube	UBERON:0001302	42.25	silver quality
monocyte	CL:0000576	40.68	gold quality
leukocyte	CL:0000738	40.30	gold quality
blood	UBERON:0000178	38.49	gold quality
sural nerve	UBERON:0015488	38.42	gold quality
metanephros cortex	UBERON:0010533	37.63	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality
apex of heart	UBERON:0002098	36.98	gold quality
ectocervix	UBERON:0012249	36.86	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
lymph node	UBERON:0000029	36.13	silver quality
popliteal artery	UBERON:0002250	36.07	gold quality
tibial artery	UBERON:0007610	35.99	gold quality
skeletal muscle tissue	UBERON:0001134	35.55	silver quality
bone marrow	UBERON:0002371	35.52	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
muscle tissue	UBERON:0002385	33.82	silver quality
gall bladder	UBERON:0002110	33.55	gold quality
thoracic aorta	UBERON:0001515	32.63	silver quality
ascending aorta	UBERON:0001496	32.55	silver quality
fallopian tube	UBERON:0003889	32.36	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6058	no	3.62
E-ANND-3	no	0.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting SPACA7, 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-6833-5P	99.50	68.93	1161
HSA-MIR-6769B-5P	98.73	64.91	1092
HSA-MIR-218-2-3P	98.08	67.21	601
HSA-MIR-299-3P	97.73	66.67	773
HSA-MIR-4491	96.53	66.20	935
HSA-MIR-4657	96.53	66.57	895
HSA-MIR-1539	92.91	60.97	91
HSA-MIR-638	83.93	64.46	66

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Spaca7	ENSMUSG00000010435
rattus_norvegicus	Spaca7	ENSRNOG00000054006

Protein

Protein identifiers

Sperm acrosome-associated protein 7 — Q96KW9 (reviewed: Q96KW9)

All UniProt accessions (4): Q96KW9, Q5T8L4, Q5T8L5, Q5T8L6

UniProt curated annotations — full annotation on UniProt →

Function. Involved in fertilization. Does not seem to play a direct role in sperm-egg binding or gamete fusion.

Subcellular location. Secreted. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Acrosome lumen.

Tissue specificity. Expressed in spermatozoa (at protein level).

RefSeq proteins (1): NP_660291* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029301	SPACA7	Family

Pfam: PF15307

UniProt features (9 total): region of interest 2, glycosylation site 2, sequence variant 2, signal peptide 1, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KW9-F1	57.99	0.00

Functional residue map

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

Glycosylation sites (2): 62, 159

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 42 (showing top): GOBP_SINGLE_FERTILIZATION, GOCC_SECRETORY_GRANULE, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, chr13q34, TGACATY_UNKNOWN, BROWN_MYELOID_CELL_DEVELOPMENT_UP, GOBP_FERTILIZATION, GOCC_LYSOSOMAL_LUMEN, GOCC_SECRETORY_VESICLE, GOCC_VESICLE_LUMEN, WGGAATGY_TEF1_Q6, GOCC_VACUOLAR_LUMEN, SANSOM_APC_TARGETS, GOCC_ACROSOMAL_VESICLE, MIKKELSEN_MCV6_ICP_WITH_H3K27ME3

GO Biological Process (1): single fertilization (GO:0007338)

GO Molecular Function (0):

GO Cellular Component (4): acrosomal vesicle (GO:0001669), extracellular region (GO:0005576), acrosomal lumen (GO:0043160), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
fertilization	1
secretory granule	1
cellular anatomical structure	1
acrosomal vesicle	1
secretory granule lumen	1
lysosomal lumen	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

144 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPACA7	SPACA9	Q96E40	604
SPACA7	GLIPR1L1	Q6UWM5	567
SPACA7	CCDC89	Q8N998	558
SPACA7	KAAG1	Q9UBP8	507
SPACA7	CFAP276	Q5T5A4	507
SPACA7	MFSD6L	Q8IWD5	497
SPACA7	SPACA4	Q8TDM5	478
SPACA7	CIMAP1A	Q96PU9	456
SPACA7	TPD52L3	Q96J77	444
SPACA7	DNAJC5B	Q9UF47	435
SPACA7	CABP1	Q9NZU7	412
SPACA7	SPACA1	Q9HBV2	401
SPACA7	CAPZA3	Q96KX2	400
SPACA7	CATSPERZ	Q9NTU4	400
SPACA7	ACRBP	Q8NEB7	390

IntAct

2 interactions, top by confidence:

A	B	Type	Score
HSPB1	SPACA7	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): SPACA7 (Two-hybrid), SPACA7 (Synthetic Lethality), SPACA7 (Positive Genetic)

ESM2 similar proteins: A0A172M4N0, A1KXM5, B3A0Q2, B3A0Q7, B6KJ32, K9N4Q4, O96001, P04144, P04671, P05686, P06796, P08961, P0CU96, P0CV08, P0CV21, P0CV36, P0CV39, P0CV40, P0CV42, P0CV43, P0CV45, P0CV46, P0CV47, P0CV48, P0CV55, P0CV57, P0CV58, P10322, P19442, P34626, P86273, Q02596, Q04807, Q09239, Q196W1, Q1HVG4, Q41121, Q5BB76, Q76KD6, Q80Y39

Diamond homologs: Q96KW9, Q9D2S4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	25
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3063290	GRCh37/hg19 13q33.1-34(chr13:104389334-115107733)x1	Pathogenic

SpliceAI

1159 predictions. Top by Δscore:

Variant	Effect	Δscore
13:112401054:T:G	acceptor_gain	1.0000
13:112401055:A:AG	acceptor_gain	1.0000
13:112401056:T:G	acceptor_gain	1.0000
13:112376478:AGG:A	donor_loss	0.9900
13:112376480:GTA:G	donor_loss	0.9900
13:112376481:T:G	donor_loss	0.9900
13:112399051:T:G	acceptor_gain	0.9900
13:112401053:A:AG	acceptor_gain	0.9900
13:112401055:ATTT:A	acceptor_gain	0.9900
13:112398139:G:GG	donor_gain	0.9700
13:112432540:A:G	donor_gain	0.9700
13:112398134:GTTAC:G	donor_gain	0.9600
13:112401058:T:TA	acceptor_gain	0.9600
13:112398135:T:G	donor_gain	0.9500
13:112432442:A:AG	acceptor_gain	0.9500
13:112432443:G:GG	acceptor_gain	0.9500
13:112376443:C:T	donor_gain	0.9400
13:112401067:A:AG	acceptor_gain	0.9400
13:112401068:G:GG	acceptor_gain	0.9400
13:112399050:AT:A	acceptor_gain	0.9300
13:112399178:A:G	donor_gain	0.9200
13:112401065:A:AG	acceptor_gain	0.9200
13:112398047:A:G	acceptor_gain	0.9100
13:112399050:A:AG	acceptor_gain	0.9100
13:112401062:A:AG	acceptor_gain	0.9100
13:112432438:CCACA:C	acceptor_loss	0.9100
13:112432439:CACA:C	acceptor_loss	0.9100
13:112432440:ACAG:A	acceptor_loss	0.9100
13:112432441:CAGAA:C	acceptor_loss	0.9100
13:112432442:A:AC	acceptor_loss	0.9100

AlphaMissense

1280 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:112432498:T:C	L167P	0.931
13:112398055:T:C	I53T	0.908
13:112398049:A:T	D51V	0.906
13:112398070:T:C	I58T	0.904
13:112398067:A:T	E57V	0.903
13:112432495:T:C	I166T	0.895
13:112398058:T:C	L54P	0.894
13:112398052:A:T	E52V	0.893
13:112376423:T:A	V13D	0.892
13:112398055:T:G	I53S	0.892
13:112393077:G:C	D51H	0.884
13:112398061:T:A	V55D	0.868
13:112376440:T:A	W19R	0.865
13:112376440:T:C	W19R	0.865
13:112376442:G:C	W19C	0.860
13:112376442:G:T	W19C	0.860
13:112398049:A:C	D51A	0.860
13:112432495:T:G	I166S	0.859
13:112398070:T:G	I58S	0.852
13:112376437:T:C	C18R	0.846
13:112393077:G:T	D51Y	0.812
13:112376434:T:C	C17R	0.809
13:112376419:T:C	F12L	0.797
13:112376421:T:A	F12L	0.797
13:112376421:T:G	F12L	0.797
13:112398067:A:C	E57A	0.793
13:112376429:T:C	L15P	0.792
13:112376426:T:C	L14P	0.789
13:112376432:T:C	L16P	0.770
13:112432489:A:T	D164V	0.756

dbSNP variants (sampled 300 via entrez): RS1000026196 (13:112391167 T>C), RS1000066880 (13:112431913 T>A), RS1000157949 (13:112405033 A>C), RS1000195009 (13:112434722 G>A), RS1000217108 (13:112424843 G>A), RS1000227571 (13:112434862 G>A,C,T), RS1000391656 (13:112418785 A>G), RS1000445729 (13:112418486 T>C), RS1000487800 (13:112404719 T>A,C), RS1000547452 (13:112399518 G>A), RS1000564079 (13:112392802 G>A), RS1000605288 (13:112423402 C>T), RS1000674288 (13:112410450 A>G), RS1000695790 (13:112388759 C>T), RS1000724832 (13:112417101 C>A)

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

1 associations (top):

Study	Trait	p-value
GCST002875_141	Diisocyanate-induced asthma	6.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006995	response to diisocyanate

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation	1
Lead	increases expression	1
Phthalic Acids	decreases methylation	1
Smoke	increases expression	1

Clinical trials (associated diseases)

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