BSPH1
protein-codingbinder of sperm protein homolog 1
Gene summary
Predicted to enable heparin binding activity. Predicted to be involved in sperm capacitation. Predicted to be located in extracellular region. Predicted to be active in cell surface. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BSPH1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001128326.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 27 | 1 | 28 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 28 | 1 | 0 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001121798.1 | 5 | MANE Select | |
| Ensembl | ENSP00000341762.3 | 5 | MANE Select | |
| RefSeq | XP_016881607.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- single fertilization
- sperm capacitation
Molecular Function
- heparin binding
Cellular Component
- extracellular region
- cell surface
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000344839
- Coding exons
- 5
- Length
- 24125
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.819 | 43 | 61.0 | 0.705 | 0.00000312 | 860 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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 (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.105
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |