SPACA3

sperm acrosome associated 3, the group of Lysozymes, c-type

Basic information

Region (hg38): 17:32970375-32997877

Links

ENSG00000141316 ∙ NCBI:124912 ∙ OMIM:612749 ∙ HGNC:16260 ∙ Uniprot:Q8IXA5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPACA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPACA3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			12	1	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1		3
Total	0	0	14	2	3

Variants in SPACA3

This is a list of pathogenic ClinVar variants found in the SPACA3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-32995436-C-T		not specified	Uncertain significance (Dec 20, 2023)
17-32995453-C-T		not specified	Uncertain significance (Mar 07, 2024)
17-32995460-T-C		not specified	Uncertain significance (Nov 15, 2021)
17-32995462-G-T		not specified	Likely benign (Jan 16, 2024)
17-32995469-G-A		not specified	Uncertain significance (Dec 27, 2023)
17-32995505-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-32995528-G-A		not specified	Uncertain significance (Sep 22, 2022)
17-32995568-G-A		not specified	Uncertain significance (Jun 18, 2024)
17-32995586-T-C		not specified	Uncertain significance (Apr 07, 2022)
17-32995681-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-32995715-A-G		not specified	Uncertain significance (Mar 01, 2024)
17-32996854-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-32996881-G-A			Benign (Nov 14, 2018)
17-32996944-A-T		not specified	Uncertain significance (Sep 14, 2023)
17-32996963-C-T		not specified	Uncertain significance (Jul 20, 2022)
17-32996966-C-T		not specified	Uncertain significance (Jun 05, 2023)
17-32996978-A-G		not specified	Uncertain significance (May 17, 2023)
17-32996987-G-A		not specified	Likely benign (Nov 10, 2022)
17-32997504-C-G		not specified	Uncertain significance (Mar 02, 2023)
17-32997505-C-T			Benign (Jul 16, 2018)
17-32997732-G-T		not specified	Uncertain significance (May 09, 2024)
17-32997763-T-C			Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPACA3	protein_coding	protein_coding	ENST00000269053	5	27502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000115	0.622	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.380	141	129	1.09	0.00000771	1377
Missense in Polyphen		37	37.455	0.98785		428
Synonymous	-0.298	54	51.3	1.05	0.00000324	441
Loss of Function	0.733	7	9.43	0.742	3.99e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000431	0.000431
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000278	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000407	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sperm surface membrane protein that may be involved in sperm-egg plasma membrane adhesion and fusion during fertilization. It could be a potential receptor for the egg oligosaccharide residue N-acetylglucosamine, which is present in the extracellular matrix over the egg plasma membrane. The processed form has no detectable bacteriolytic activity in vitro. {ECO:0000269|PubMed:12606493}.

Recessive Scores

• pRec: 0.0728

Intolerance Scores

• loftool: 0.560
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.79

Haploinsufficiency Scores

• pHI: 0.0562
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0781

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Spaca3
• Phenotype: normal phenotype

Gene ontology

• Biological process: fusion of sperm to egg plasma membrane involved in single fertilization;sperm-egg recognition;monocyte activation;positive regulation of macrophage activation;positive regulation of phagocytosis;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium
• Cellular component: acrosomal membrane;extracellular region;integral component of membrane;secretory granule;acrosomal matrix
• Molecular function: lysozyme activity;protein binding