IZUMO1

izumo sperm-oocyte fusion 1, the group of Ig-like cell adhesion molecule family|IZUMO family

Basic information

Region (hg38): 19:48740852-48746909

Links

ENSG00000182264 ∙ NCBI:284359 ∙ OMIM:609278 ∙ HGNC:28539 ∙ Uniprot:Q8IYV9 ∙ 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 IZUMO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IZUMO1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in IZUMO1

This is a list of pathogenic ClinVar variants found in the IZUMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48741314-C-A		not specified	Uncertain significance (Jun 16, 2024)
19-48741314-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-48741316-G-C		not specified	Uncertain significance (Mar 25, 2024)
19-48741379-G-A		not specified	Uncertain significance (Nov 08, 2022)
19-48741403-G-A		not specified	Uncertain significance (Jul 02, 2024)
19-48741443-G-A		not specified	Uncertain significance (May 07, 2024)
19-48741478-A-G		not specified	Uncertain significance (Feb 06, 2023)
19-48741849-G-A		not specified	Uncertain significance (Nov 10, 2022)
19-48741896-G-A		not specified	Uncertain significance (Jan 20, 2023)
19-48741911-G-C		not specified	Uncertain significance (Oct 08, 2024)
19-48741918-A-C		not specified	Uncertain significance (Jan 17, 2023)
19-48741930-T-A		not specified	Uncertain significance (Mar 07, 2024)
19-48742234-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-48743475-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-48744467-C-A		not specified	Uncertain significance (Aug 28, 2024)
19-48744528-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-48745630-A-G		not specified	Likely benign (Mar 13, 2023)
19-48745646-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-48745715-G-A		not specified	Uncertain significance (Jun 28, 2023)
19-48745850-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IZUMO1	protein_coding	protein_coding	ENST00000332955	9	6058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.04e-8	0.525	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	165	210	0.786	0.0000121	2290
Missense in Polyphen		54	67.365	0.80161		761
Synonymous	1.04	78	90.6	0.861	0.00000616	671
Loss of Function	1.01	14	18.7	0.748	9.93e-7	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000760	0.000760
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000272	0.000272
South Asian	0.000294	0.000294
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential sperm cell-surface protein required for fertilization by acting as a ligand for IZUMO1R/JUNO receptor on egg. The IZUMO1:IZUMO1R/JUNO interaction is a necessary adhesion event between sperm and egg that is required for fertilization but is not sufficient for cell fusion. The ligand-receptor interaction probably does not act as a membrane 'fusogen'. {ECO:0000269|PubMed:15759005}.
• Pathway: Fertilization;Reproduction;Sperm:Oocyte Membrane Binding (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.608
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.0209
• hipred: N
• hipred_score: 0.207
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Izumo1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: cell adhesion;single fertilization;fusion of sperm to egg plasma membrane involved in single fertilization;heterotypic cell-cell adhesion;sperm-egg recognition
• Cellular component: acrosomal membrane;plasma membrane;integral component of membrane
• Molecular function: signaling receptor binding;protein binding;protein homodimerization activity;protein binding involved in heterotypic cell-cell adhesion