OMG

oligodendrocyte myelin glycoprotein

Basic information

Region (hg38): 17:31272013-31297539

Links

ENSG00000126861 ∙ NCBI:4974 ∙ OMIM:164345 ∙ HGNC:8135 ∙ Uniprot:P23515 ∙ 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 OMG gene.

• not_specified (42 variants)
• not_provided (11 variants)
• OMG-related_disorder (3 variants)
• Cardiovascular_phenotype (1 variants)
• Hereditary_cancer-predisposing_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OMG gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002544.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				8	1	9
missense			41	4		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	12	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OMG	protein_coding	protein_coding	ENST00000247271	1	25527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0288	125721	0	8	125729	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	162	217	0.748	0.0000101	2899
Missense in Polyphen		62	97.246	0.63756		1327
Synonymous	0.719	75	83.4	0.900	0.00000397	889
Loss of Function	3.07	0	11.0	0.00	5.42e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000330	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule contributing to the interactive process required for myelination in the central nervous system.
• Pathway: Spinal Cord Injury;Signal Transduction;Death Receptor Signalling;Axonal growth inhibition (RHOA activation);p75NTR regulates axonogenesis;p75 NTR receptor-mediated signalling;p75(NTR)-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.190

Intolerance Scores

• loftool: 0.236
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.394
• hipred: Y
• hipred_score: 0.546
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.594

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Omg
• Phenotype: homeostasis/metabolism phenotype; normal phenotype

Gene ontology

• Biological process: cell adhesion;neuron projection regeneration;negative regulation of axonogenesis
• Cellular component: plasma membrane;anchored component of membrane