SPA17

sperm autoantigenic protein 17

Basic information

Region (hg38): 11:124673844-124697518

Links

ENSG00000064199 ∙ NCBI:53340 ∙ OMIM:608621 ∙ HGNC:11210 ∙ Uniprot:Q15506 ∙ 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 SPA17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPA17 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in SPA17

This is a list of pathogenic ClinVar variants found in the SPA17 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124675271-A-G		not specified	Uncertain significance (Dec 01, 2022)
11-124675305-A-T		not specified	Uncertain significance (Apr 12, 2022)
11-124675322-C-T		not specified	Uncertain significance (Apr 11, 2023)
11-124675323-T-C		not specified	Uncertain significance (May 18, 2023)
11-124675340-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-124675388-T-C		not specified	Uncertain significance (Nov 11, 2024)
11-124675413-G-C		not specified	Uncertain significance (Jul 29, 2022)
11-124675415-G-C		not specified	Uncertain significance (Dec 21, 2023)
11-124681395-A-G		not specified	Uncertain significance (Mar 08, 2025)
11-124681434-G-A		not specified	Uncertain significance (Sep 04, 2024)
11-124681446-A-G		not specified	Uncertain significance (Jan 09, 2025)
11-124691723-C-T		not specified	Uncertain significance (Sep 02, 2024)
11-124691726-A-G		not specified	Likely benign (Mar 19, 2024)
11-124691753-A-G		not specified	Uncertain significance (Sep 09, 2021)
11-124691762-G-C		not specified	Uncertain significance (Aug 15, 2024)
11-124694324-G-A		not specified	Uncertain significance (Sep 25, 2024)
11-124694369-G-A		not specified	Uncertain significance (Dec 12, 2023)
11-124694387-G-A		not specified	Uncertain significance (Mar 07, 2025)
11-124694439-A-C		not specified	Uncertain significance (Oct 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPA17	protein_coding	protein_coding	ENST00000532692	4	23721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00662	0.767	125733	0	11	125744	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.158	86	82.0	1.05	0.00000434	1005
Missense in Polyphen		30	33.413	0.89784		371
Synonymous	-0.143	29	28.0	1.03	0.00000151	265
Loss of Function	0.902	4	6.48	0.617	3.60e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000128
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000221	0.000217
South Asian	0.00	0.00
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sperm surface zona pellucida binding protein. Helps to bind spermatozoa to the zona pellucida with high affinity. Might function in binding zona pellucida and carbohydrates (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0514

Intolerance Scores

• loftool: 0.495
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.0367
• hipred: N
• hipred_score: 0.171
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spa17

Zebrafish Information Network

• Gene name: spa17
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: epithelial cilium movement;spermatogenesis;single fertilization;binding of sperm to zona pellucida
• Cellular component: cytoplasm;cilium;external side of plasma membrane;motile cilium;sperm fibrous sheath;sperm principal piece
• Molecular function: protein binding;calmodulin binding