SPACA4

sperm acrosome associated 4, the group of LY6/PLAUR domain containing

Basic information

Region (hg38): 19:48606742-48607714

Links

ENSG00000177202 ∙ NCBI:171169 ∙ OMIM:609932 ∙ HGNC:16441 ∙ Uniprot:Q8TDM5 ∙ 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 SPACA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPACA4 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						0
missense			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in SPACA4

This is a list of pathogenic ClinVar variants found in the SPACA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48607028-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-48607031-C-T		not specified	Uncertain significance (Oct 16, 2023)
19-48607034-G-T		not specified	Uncertain significance (Mar 19, 2024)
19-48607036-G-A		not specified	Uncertain significance (Sep 12, 2024)
19-48607048-G-A		not specified	Likely benign (Nov 28, 2024)
19-48607124-C-T		not specified	Uncertain significance (Oct 26, 2021)
19-48607135-G-T		not specified	Uncertain significance (Nov 10, 2022)
19-48607142-C-T		not specified	Uncertain significance (Oct 16, 2024)
19-48607255-G-A		not specified	Uncertain significance (Dec 07, 2023)
19-48607328-T-C		not specified	Uncertain significance (Aug 12, 2021)
19-48607337-C-T		not specified	Likely benign (Jul 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPACA4	protein_coding	protein_coding	ENST00000321762	1	971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.283	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	57	79.8	0.715	0.00000521	781
Missense in Polyphen		17	29.099	0.58421		281
Synonymous	0.958	31	38.6	0.804	0.00000305	269
Loss of Function	0.152	0	0.0268	0.00	9.19e-10	1

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
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.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.306
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.238
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spaca4

Gene ontology

• Biological process: cell adhesion
• Cellular component: acrosomal vesicle;extracellular region;plasma membrane;anchored component of membrane