IZUMO4

IZUMO family member 4, the group of IZUMO family

Basic information

Region (hg38): 19:2096429-2099593

Previous symbols: [ "C19orf36" ]

Links

ENSG00000099840 ∙ NCBI:113177 ∙ OMIM:618897 ∙ HGNC:26950 ∙ Uniprot:Q1ZYL8 ∙ 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 IZUMO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IZUMO4 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	1		22
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	1	0

Variants in IZUMO4

This is a list of pathogenic ClinVar variants found in the IZUMO4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-2096971-G-T		not specified	Uncertain significance (Nov 22, 2022)
19-2096993-C-A		not specified	Uncertain significance (May 24, 2023)
19-2096997-T-C		not specified	Uncertain significance (Sep 12, 2023)
19-2097072-G-A		not specified	Uncertain significance (Mar 08, 2025)
19-2097117-G-T		not specified	Uncertain significance (Feb 11, 2022)
19-2097129-A-G		not specified	Uncertain significance (Dec 04, 2024)
19-2097157-A-T		not specified	Uncertain significance (Apr 09, 2024)
19-2097257-G-A		not specified	Uncertain significance (Mar 06, 2025)
19-2097276-C-G		not specified	Uncertain significance (Jan 23, 2023)
19-2097457-G-A		not specified	Uncertain significance (Jun 28, 2022)
19-2097932-G-A		not specified	Uncertain significance (Feb 05, 2024)
19-2097949-C-A		not specified	Uncertain significance (Feb 24, 2025)
19-2098091-C-T		not specified	Uncertain significance (Feb 21, 2025)
19-2098102-G-T		not specified	Uncertain significance (Jul 02, 2024)
19-2098289-C-T		not specified	Uncertain significance (Oct 16, 2023)
19-2098292-C-T		not specified	Uncertain significance (Apr 06, 2023)
19-2098295-C-T		not specified	Uncertain significance (Jun 18, 2024)
19-2098299-G-C		not specified	Uncertain significance (Jul 26, 2024)
19-2099014-G-A		not specified	Uncertain significance (Nov 14, 2023)
19-2099020-C-T		not specified	Uncertain significance (Dec 05, 2024)
19-2099023-C-T		not specified	Uncertain significance (May 27, 2022)
19-2099278-G-A		not specified	Uncertain significance (Apr 20, 2024)
19-2099293-A-G		not specified	Uncertain significance (Sep 06, 2022)
19-2099311-T-C		not specified	Uncertain significance (Jun 30, 2024)
19-2099328-T-C		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IZUMO4	protein_coding	protein_coding	ENST00000395301	10	3213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-14	0.00544	125664	1	80	125745	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.891	168	138	1.21	0.00000762	1519
Missense in Polyphen		75	65.177	1.1507		778
Synonymous	-1.82	78	60.0	1.30	0.00000367	420
Loss of Function	-0.692	19	16.0	1.19	6.87e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000273	0.000270
Ashkenazi Jewish	0.00	0.00
East Asian	0.000327	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.000327	0.000326
South Asian	0.00125	0.00121
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.333
• hipred: N
• hipred_score: 0.146
• ghis: 0.533

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Izumo4

Gene ontology

• Cellular component: extracellular region;nucleus