SPACA1

sperm acrosome associated 1

Basic information

Region (hg38): 6:88047840-88066838

Links

ENSG00000118434 ∙ NCBI:81833 ∙ OMIM:612739 ∙ HGNC:14967 ∙ Uniprot:Q9HBV2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 85	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	34172998

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPACA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPACA1 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	0

Variants in SPACA1

This is a list of pathogenic ClinVar variants found in the SPACA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-88047958-G-A		Spermatogenic failure 85	Pathogenic (Aug 25, 2023)
6-88048003-C-T		not specified	Uncertain significance (Nov 13, 2023)
6-88048065-A-C		not specified	Uncertain significance (Feb 16, 2023)
6-88048087-A-G		not specified	Uncertain significance (Oct 26, 2021)
6-88053955-G-A		not specified	Uncertain significance (May 02, 2024)
6-88053973-T-C		not specified	Uncertain significance (Jan 29, 2024)
6-88053981-G-A		not specified	Uncertain significance (Jan 17, 2024)
6-88053984-A-C		not specified	Uncertain significance (Aug 08, 2023)
6-88053990-A-G		not specified	Uncertain significance (Mar 06, 2023)
6-88058748-G-C		not specified	Uncertain significance (Dec 14, 2023)
6-88058791-A-C		not specified	Uncertain significance (Nov 09, 2023)
6-88058796-A-G		not specified	Uncertain significance (Jan 03, 2022)
6-88059489-G-A		not specified	Uncertain significance (Nov 12, 2021)
6-88059505-G-A		not specified	Likely benign (Aug 01, 2022)
6-88059529-A-G		not specified	Uncertain significance (Feb 28, 2024)
6-88059535-T-A		not specified	Uncertain significance (Jul 12, 2023)
6-88064108-T-C		not specified	Uncertain significance (May 18, 2022)
6-88064120-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-88064171-T-C		not specified	Uncertain significance (Jun 22, 2024)
6-88064174-T-C		not specified	Uncertain significance (Mar 18, 2024)
6-88064177-G-A		not specified	Uncertain significance (Apr 19, 2023)
6-88064198-T-G		not specified	Uncertain significance (Apr 09, 2024)
6-88066194-G-T		not specified	Uncertain significance (May 10, 2022)
6-88066207-G-A		not specified	Uncertain significance (Jun 03, 2022)
6-88066243-A-C		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPACA1	protein_coding	protein_coding	ENST00000237201	7	19044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0227	0.964	125722	0	4	125726	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.676	149	174	0.856	0.0000102	1900
Missense in Polyphen		45	59.788	0.75265		751
Synonymous	1.11	60	72.0	0.834	0.00000525	571
Loss of Function	2.16	5	13.6	0.368	5.74e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000624	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000659	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000945	0.00000879
Middle Eastern	0.0000659	0.0000544
South Asian	0.0000342	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in acrosome expansion and establishment of normal sperm morphology during spermatogenesis (By similarity). Important for male fertility (PubMed:11870081). {ECO:0000250|UniProtKB:Q9DA48, ECO:0000269|PubMed:11870081}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.292
• rvis_EVS: -0.29
• rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

• pHI: 0.107
• hipred: N
• hipred_score: 0.200
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spaca1
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: acrosome assembly
• Cellular component: inner acrosomal membrane;acrosomal membrane;integral component of membrane