SPACA9

sperm acrosome associated 9

Basic information

Region (hg38): 9:132878027-132890201

Previous symbols: [ "C9orf9" ]

Links

ENSG00000165698 ∙ NCBI:11092 ∙ OMIM:618552 ∙ HGNC:1367 ∙ Uniprot:Q96E40 ∙ 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 SPACA9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPACA9 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1		5
Total	0	0	6	1	0

Variants in SPACA9

This is a list of pathogenic ClinVar variants found in the SPACA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132878221-G-C		not specified	Uncertain significance (Feb 17, 2024)
9-132878222-G-C		not specified	Uncertain significance (Nov 17, 2023)
9-132878222-G-T		not specified	Uncertain significance (Jan 31, 2022)
9-132878231-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-132878246-T-C		not specified	Likely benign (Jun 24, 2022)
9-132883981-G-A		not specified	Uncertain significance (Oct 12, 2021)
9-132888386-G-T		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPACA9	protein_coding	protein_coding	ENST00000350499	4	12175

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000439	0.420	125631	0	117	125748	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.362	118	107	1.10	0.00000680	1119
Missense in Polyphen		53	44.598	1.1884		447
Synonymous	-0.377	50	46.7	1.07	0.00000339	305
Loss of Function	0.298	7	7.90	0.886	4.33e-7	88

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00162
Ashkenazi Jewish	0.00189	0.00189
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000325	0.000316
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.00103	0.000978

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.101

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.267
• ghis: 0.579

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spaca9

Gene ontology

• Cellular component: acrosomal vesicle;nucleus;cytoplasmic microtubule;ciliary basal body;sperm flagellum;ciliary base
• Molecular function: protein binding;calcium-dependent protein binding