SPESP1

sperm equatorial segment protein 1

Basic information

Region (hg38): 15:68818221-68946811

Links

ENSG00000258484 ∙ NCBI:246777 ∙ OMIM:609399 ∙ HGNC:15570 ∙ Uniprot:Q6UW49 ∙ 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 SPESP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPESP1 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			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	0

Variants in SPESP1

This is a list of pathogenic ClinVar variants found in the SPESP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-68930679-C-T		not specified	Uncertain significance (Aug 15, 2023)
15-68945622-G-C		not specified	Uncertain significance (Jun 10, 2024)
15-68945634-A-G		not specified	Uncertain significance (Nov 10, 2024)
15-68945695-G-A		not specified	Uncertain significance (Jan 03, 2022)
15-68945695-G-T		not specified	Uncertain significance (Sep 03, 2024)
15-68945722-A-G		not specified	Uncertain significance (Aug 13, 2021)
15-68945723-T-G		not specified	Uncertain significance (Oct 06, 2023)
15-68945798-T-A		not specified	Uncertain significance (Jul 20, 2021)
15-68945806-C-G		not specified	Uncertain significance (Mar 06, 2023)
15-68945833-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-68945857-C-T		not specified	Likely benign (Sep 30, 2024)
15-68945862-A-G		not specified	Uncertain significance (Jan 23, 2024)
15-68945865-G-C		not specified	Uncertain significance (Aug 30, 2021)
15-68945888-T-G		not specified	Uncertain significance (Mar 31, 2023)
15-68945946-C-A		not specified	Uncertain significance (Apr 18, 2024)
15-68945946-C-T		not specified	Uncertain significance (Nov 27, 2024)
15-68945952-A-G		not specified	Uncertain significance (Nov 26, 2024)
15-68945953-T-C		not specified	Uncertain significance (Dec 30, 2023)
15-68946055-T-C		not specified	Uncertain significance (Feb 08, 2023)
15-68946111-T-G		not specified	Uncertain significance (Jun 19, 2024)
15-68946132-C-G		not specified	Uncertain significance (Apr 29, 2024)
15-68946133-C-A		not specified	Uncertain significance (Apr 25, 2023)
15-68946168-G-A		not specified	Likely benign (Aug 19, 2023)
15-68946187-C-T		not specified	Uncertain significance (Dec 06, 2022)
15-68946228-G-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPESP1	protein_coding	protein_coding	ENST00000310673	2	128591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.395	0.482	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.187	176	183	0.961	0.00000915	2257
Missense in Polyphen		45	45.628	0.98625		612
Synonymous	0.613	64	70.6	0.907	0.00000395	696
Loss of Function	0.933	0	1.01	0.00	4.21e-8	15

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: Involved in fertilization ability of sperm. {ECO:0000250|UniProtKB:Q9D5A0}.

Recessive Scores

• pRec: 0.0734

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• pHI: 0.0583
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spesp1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;acrosome reaction;fusion of sperm to egg plasma membrane involved in single fertilization;fertilization;sperm-egg recognition
• Cellular component: acrosomal vesicle