ELSPBP1

epididymal sperm binding protein 1

Basic information

Region (hg38): 19:47994632-48025154

Links

ENSG00000169393 ∙ NCBI:64100 ∙ OMIM:607443 ∙ HGNC:14417 ∙ Uniprot:Q96BH3 ∙ 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 ELSPBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELSPBP1 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			12			12
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	0	0

Variants in ELSPBP1

This is a list of pathogenic ClinVar variants found in the ELSPBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48008675-G-A		not specified	Uncertain significance (May 14, 2024)
19-48008704-A-G		not specified	Uncertain significance (Oct 11, 2024)
19-48008723-A-G		not specified	Uncertain significance (May 24, 2023)
19-48008734-G-A		not specified	Uncertain significance (Mar 27, 2023)
19-48014171-G-T		not specified	Uncertain significance (Jun 07, 2024)
19-48014215-G-C		not specified	Uncertain significance (Jun 13, 2023)
19-48015969-A-C		not specified	Uncertain significance (Feb 28, 2024)
19-48015975-T-G		not specified	Uncertain significance (Feb 10, 2023)
19-48015992-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-48019757-C-A		not specified	Uncertain significance (Jan 26, 2023)
19-48019781-G-C		not specified	Uncertain significance (Aug 03, 2022)
19-48019810-C-A		not specified	Uncertain significance (May 09, 2023)
19-48019856-T-C		not specified	Uncertain significance (Feb 28, 2024)
19-48022212-T-C		not specified	Uncertain significance (Sep 16, 2021)
19-48022254-G-A		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELSPBP1	protein_coding	protein_coding	ENST00000339841	5	30503

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.52e-11	0.0296	125655	1	87	125743	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00763	117	117	0.998	0.00000558	1478
Missense in Polyphen		45	47.331	0.95076		612
Synonymous	0.184	45	46.6	0.966	0.00000286	363
Loss of Function	-0.262	16	14.9	1.07	7.81e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000851	0.000851
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.000163	0.000163
South Asian	0.00144	0.00141
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to spermatozoa upon ejaculation and may play a role in sperm capacitation. Has phosphorylcholine-binding activity (By similarity). {ECO:0000250}.
• Pathway: miRs in Muscle Cell Differentiation;nfat and hypertrophy of the heart (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.657
• rvis_EVS: 1.84
• rvis_percentile_EVS: 97.06

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.166

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Gene ontology

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