BSPH1

binder of sperm protein homolog 1

Basic information

Region (hg38): 19:47968046-47992170

Links

ENSG00000188334 ∙ NCBI:100131137 ∙ OMIM:612213 ∙ HGNC:33906 ∙ Uniprot:Q075Z2 ∙ 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 BSPH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BSPH1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in BSPH1

This is a list of pathogenic ClinVar variants found in the BSPH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47976735-G-C		not specified	Uncertain significance (Aug 05, 2024)
19-47976755-G-A		not specified	Uncertain significance (Jun 05, 2023)
19-47976785-T-C		not specified	Uncertain significance (Dec 15, 2023)
19-47976819-G-A		not specified	Uncertain significance (Apr 27, 2023)
19-47976844-G-C		not specified	Likely benign (Apr 18, 2024)
19-47977394-A-C		not specified	Uncertain significance (Nov 22, 2023)
19-47977423-C-G		not specified	Uncertain significance (Dec 03, 2024)
19-47977450-A-G		not specified	Uncertain significance (Apr 17, 2023)
19-47977493-C-T		not specified	Uncertain significance (Jan 31, 2023)
19-47980940-A-T		not specified	Uncertain significance (Oct 29, 2021)
19-47992032-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-47992044-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-47992050-G-A		not specified	Uncertain significance (Dec 23, 2024)
19-47992066-G-A		not specified	Uncertain significance (Jul 12, 2023)
19-47992071-A-G		not specified	Uncertain significance (Sep 02, 2024)
19-47992075-A-G		not specified	Uncertain significance (Mar 01, 2025)
19-47992078-C-G		not specified	Uncertain significance (Jan 29, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BSPH1	protein_coding	protein_coding	ENST00000344839	5	24125

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0165	0.895	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.819	43	61.0	0.705	0.00000312	860
Missense in Polyphen		11	15.967	0.68891		218
Synonymous	1.22	16	23.5	0.681	0.00000135	218
Loss of Function	1.43	4	8.51	0.470	4.39e-7	119

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: Binds sperm in vitro and promotes sperm capacitation. Specifically promotes capacitation induced by high density lipoproteins (HDLs). Also binds heparin, phospholipid liposomes, and weakly to gelatin. Does not bind chondroitin sulfate B. {ECO:0000250|UniProtKB:Q3UW26}.

Recessive Scores

• pRec: 0.0990

Intolerance Scores

• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.79

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.105

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bsph1

Gene ontology

• Biological process: single fertilization;sperm capacitation
• Cellular component: extracellular region;cell surface
• Molecular function: heparin binding