SPACA7

sperm acrosome associated 7

Basic information

Region (hg38): 13:112376354-112434689

Previous symbols: [ "C13orf28" ]

Links

ENSG00000153498 ∙ NCBI:122258 ∙ ∙ HGNC:29575 ∙ Uniprot:Q96KW9 ∙ 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 SPACA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPACA7 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	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	0

Variants in SPACA7

This is a list of pathogenic ClinVar variants found in the SPACA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-112376407-G-A		not specified	Uncertain significance (Aug 28, 2023)
13-112376452-G-A		not specified	Uncertain significance (Sep 09, 2021)
13-112376458-C-T		not specified	Uncertain significance (Sep 22, 2022)
13-112376470-G-A		not specified	Uncertain significance (Aug 02, 2021)
13-112398053-A-T		not specified	Uncertain significance (Feb 16, 2023)
13-112398103-T-C		not specified	Likely benign (Dec 30, 2023)
13-112398119-A-C			Likely benign (Jun 01, 2023)
13-112398133-C-T		not specified	Uncertain significance (Apr 13, 2023)
13-112399080-G-A		not specified	Uncertain significance (Apr 07, 2022)
13-112399091-A-C		not specified	Uncertain significance (Aug 14, 2023)
13-112401101-C-A		not specified	Uncertain significance (Jan 04, 2024)
13-112401131-T-C		not specified	Uncertain significance (Feb 09, 2023)
13-112432509-G-A		not specified	Uncertain significance (Dec 01, 2022)
13-112434491-T-G		not specified	Likely benign (Apr 07, 2022)
13-112434499-A-C		not specified	Uncertain significance (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPACA7	protein_coding	protein_coding	ENST00000283550	7	58371

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000133	0.391	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.121	100	103	0.967	0.00000540	1267
Missense in Polyphen		22	25.413	0.8657		321
Synonymous	-0.816	46	39.5	1.17	0.00000227	350
Loss of Function	0.530	10	12.0	0.835	6.06e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000648	0.000647
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in fertilization. Seems not to play a direct role in sperm-egg binding or gamete fusion. {ECO:0000250|UniProtKB:Q9D2S4}.

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.123
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spaca7
• Phenotype: normal phenotype

Gene ontology

• Biological process: single fertilization
• Cellular component: acrosomal vesicle;extracellular region;acrosomal lumen