IZUMO2

IZUMO family member 2, the group of IZUMO family

Basic information

Region (hg38): 19:50152548-50163281

Previous symbols: [ "C19orf41" ]

Links

ENSG00000161652 ∙ NCBI:126123 ∙ OMIM:618895 ∙ HGNC:28518 ∙ Uniprot:Q6UXV1 ∙ 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 IZUMO2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IZUMO2 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in IZUMO2

This is a list of pathogenic ClinVar variants found in the IZUMO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50154607-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-50154615-A-G		not specified	Uncertain significance (May 05, 2023)
19-50154640-C-A		not specified	Uncertain significance (Dec 25, 2024)
19-50154649-G-A		not specified	Likely benign (Feb 18, 2025)
19-50154667-G-C		not specified	Uncertain significance (Sep 16, 2021)
19-50154675-G-A		not specified	Likely benign (Aug 23, 2021)
19-50154709-C-T		not specified	Likely benign (Sep 22, 2022)
19-50154711-C-T		not specified	Uncertain significance (Aug 14, 2024)
19-50154720-C-T		not specified	Uncertain significance (Mar 26, 2024)
19-50154724-C-T		not specified	Uncertain significance (Jan 23, 2024)
19-50158307-T-C		not specified	Uncertain significance (Jan 24, 2025)
19-50158316-G-C		not specified	Uncertain significance (Jul 13, 2022)
19-50158339-T-G		not specified	Uncertain significance (Aug 17, 2021)
19-50158343-G-C		not specified	Uncertain significance (Nov 26, 2024)
19-50159235-A-C		not specified	Uncertain significance (Jun 06, 2022)
19-50159239-T-C		not specified	Uncertain significance (Nov 09, 2024)
19-50159247-C-A		not specified	Uncertain significance (Oct 24, 2023)
19-50159574-G-A		not specified	Uncertain significance (Aug 08, 2023)
19-50162744-A-G		not specified	Uncertain significance (Apr 30, 2024)
19-50162778-T-C		not specified	Uncertain significance (Jul 06, 2021)
19-50162975-C-T		not specified	Uncertain significance (Aug 27, 2024)
19-50162978-A-T		not specified	Uncertain significance (Feb 26, 2024)
19-50162982-G-T		not specified	Uncertain significance (Dec 03, 2021)
19-50163011-C-T		not specified	Uncertain significance (Dec 13, 2023)
19-50163118-G-A		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IZUMO2	protein_coding	protein_coding	ENST00000293405	7	10648

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000247	0.766	124732	0	67	124799	0.000268

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.273	121	130	0.933	0.00000765	1409
Missense in Polyphen		2	5.4026	0.37019		52
Synonymous	-0.621	64	58.0	1.10	0.00000361	444
Loss of Function	1.15	9	13.6	0.662	7.74e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00102
Ashkenazi Jewish	0.000794	0.000795
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000232	0.000230
Middle Eastern	0.00	0.00
South Asian	0.000231	0.000229
Other	0.000172	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Fertilization;Reproduction;Sperm:Oocyte Membrane Binding (Consensus)

Recessive Scores

• pRec: 0.0595

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.0627
• hipred: N
• hipred_score: 0.146
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Mouse Genome Informatics

• Gene name: Izumo2

Gene ontology

• Cellular component: integral component of membrane