VMO1

vitelline membrane outer layer 1 homolog

Basic information

Region (hg38): 17:4785285-4786433

Links

ENSG00000182853 ∙ NCBI:284013 ∙ ∙ HGNC:30387 ∙ Uniprot:Q7Z5L0 ∙ 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 VMO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VMO1 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in VMO1

This is a list of pathogenic ClinVar variants found in the VMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4785382-A-T		not specified	Uncertain significance (Jan 29, 2024)
17-4785387-G-A		not specified	Likely benign (Sep 01, 2021)
17-4785391-C-A		not specified	Uncertain significance (Oct 06, 2021)
17-4785399-G-T		not specified	Uncertain significance (Apr 07, 2023)
17-4785485-A-T		not specified	Uncertain significance (Aug 30, 2021)
17-4785493-C-G		not specified	Uncertain significance (Feb 27, 2023)
17-4785510-C-T		not specified	Uncertain significance (Nov 21, 2022)
17-4785532-A-C		not specified	Uncertain significance (May 15, 2024)
17-4785547-C-T		not specified	Uncertain significance (Nov 09, 2023)
17-4785561-G-C		not specified	Uncertain significance (Aug 16, 2021)
17-4785609-A-G		not specified	Uncertain significance (Nov 18, 2023)
17-4785622-C-G		not specified	Uncertain significance (Mar 25, 2024)
17-4785636-A-G		not specified	Uncertain significance (Dec 12, 2023)
17-4785639-G-T		not specified	Uncertain significance (Jan 26, 2022)
17-4785999-C-G		not specified	Uncertain significance (May 07, 2024)
17-4786025-C-A		not specified	Uncertain significance (Mar 01, 2024)
17-4786030-G-A		not specified	Likely benign (Jan 24, 2024)
17-4786184-A-C		not specified	Uncertain significance (Dec 19, 2022)
17-4786216-T-C		not specified	Uncertain significance (Sep 06, 2022)
17-4786247-T-C		not specified	Uncertain significance (May 07, 2024)
17-4786339-G-A		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VMO1	protein_coding	protein_coding	ENST00000328739	3	1149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000212	0.158	125715	0	32	125747	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.173	139	133	1.04	0.00000852	1282
Missense in Polyphen		54	56.511	0.95557		581
Synonymous	1.20	53	65.4	0.811	0.00000506	432
Loss of Function	-0.417	8	6.82	1.17	2.94e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000456	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0855

Intolerance Scores

• loftool: 0.844
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.0680
• hipred: N
• hipred_score: 0.216
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00582

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vmo1

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular exosome
• Molecular function: molecular_function