SPAM1

sperm adhesion molecule 1, the group of Hyaluronidases

Basic information

Region (hg38): 7:123925237-123971414

Links

ENSG00000106304 ∙ ∙ OMIM:600930 ∙ HGNC:11217 ∙ Uniprot:P38567 ∙ 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 SPAM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPAM1 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	4		34
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	4	0

Variants in SPAM1

This is a list of pathogenic ClinVar variants found in the SPAM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-123953577-G-A		not specified	Uncertain significance (Dec 11, 2024)
7-123953628-G-A		not specified	Uncertain significance (Jul 30, 2024)
7-123953737-C-G		not specified	Uncertain significance (Mar 30, 2024)
7-123953809-G-A		not specified	Likely benign (Mar 26, 2024)
7-123953815-A-G		not specified	Uncertain significance (Jul 06, 2024)
7-123953818-C-G		not specified	Uncertain significance (Feb 20, 2025)
7-123953944-A-T		not specified	Uncertain significance (Jan 31, 2024)
7-123953991-G-A		not specified	Uncertain significance (Feb 26, 2024)
7-123954024-C-A		not specified	Uncertain significance (Nov 18, 2023)
7-123954186-T-A		not specified	Uncertain significance (Oct 25, 2024)
7-123954197-A-C		not specified	Uncertain significance (Apr 24, 2024)
7-123954198-C-A		not specified	Uncertain significance (Aug 14, 2024)
7-123954312-G-A		not specified	Uncertain significance (Nov 07, 2024)
7-123954340-C-T		not specified	Uncertain significance (Mar 03, 2025)
7-123954381-C-T		not specified	Likely benign (Oct 04, 2022)
7-123954403-T-C		not specified	Uncertain significance (Jun 13, 2022)
7-123954405-C-T		not specified	Uncertain significance (Feb 28, 2025)
7-123954412-G-A		not specified	Uncertain significance (Sep 11, 2024)
7-123954443-A-G		not specified	Uncertain significance (Feb 28, 2023)
7-123954466-C-T		not specified	Uncertain significance (Dec 22, 2023)
7-123954481-C-T		not specified	Uncertain significance (May 13, 2022)
7-123954483-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-123954484-G-A		not specified	Uncertain significance (Feb 13, 2024)
7-123955039-G-T		not specified	Uncertain significance (Apr 11, 2023)
7-123955040-C-T		not specified	Likely benign (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPAM1	protein_coding	protein_coding	ENST00000340011	4	46183

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-10	0.227	125439	0	23	125462	0.0000917

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.997	224	270	0.829	0.0000130	3387
Missense in Polyphen		71	89.585	0.79254		1091
Synonymous	1.30	77	92.9	0.829	0.00000469	964
Loss of Function	0.729	17	20.6	0.827	0.00000110	248

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)	0.00000938	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.000687	0.000687
Other	0.000164	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in sperm-egg adhesion. Upon fertilization sperm must first penetrate a layer of cumulus cells that surrounds the egg before reaching the zona pellucida. The cumulus cells are embedded in a matrix containing hyaluronic acid which is formed prior to ovulation. This protein aids in penetrating the layer of cumulus cells by digesting hyaluronic acid. {ECO:0000269|PubMed:8282124}.
• Pathway: Glycosaminoglycan degradation - Homo sapiens (human);Interaction With Cumulus Cells;Fertilization;chondroitin sulfate degradation (metazoa);Reproduction;dermatan sulfate degradation (metazoa) (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.991
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.16

Haploinsufficiency Scores

• pHI: 0.0854
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hyal5

Gene ontology

• Biological process: carbohydrate metabolic process;cell adhesion;binding of sperm to zona pellucida;fusion of sperm to egg plasma membrane involved in single fertilization;sperm-egg recognition
• Cellular component: plasma membrane;anchored component of membrane
• Molecular function: hyalurononglucosaminidase activity