OMG

oligodendrocyte myelin glycoprotein

Basic information

Region (hg38): 17:31272012-31297539

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.

• Inborn genetic diseases (9 variants)
• not provided (5 variants)
• not specified (2 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.

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				1	1	2
missense			10	3		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	10	4	2

Variants in OMG

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

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

Position	Type	Phenotype	Significance	ClinVar
17-31295014-C-G		not specified	Uncertain significance (Apr 06, 2022)
17-31295028-A-G		OMG-related disorder	Benign/Likely benign (May 24, 2019)
17-31295066-C-G			Likely benign (Sep 01, 2022)
17-31295081-A-C		OMG-related disorder	Likely benign (Mar 27, 2020)
17-31295094-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-31295099-T-C			Likely benign (Jun 21, 2018)
17-31295110-T-C		Hereditary cancer-predisposing syndrome	Likely benign (Apr 01, 2024)
17-31295136-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-31295154-A-G		not specified	Uncertain significance (Nov 07, 2022)
17-31295199-A-G		not specified	Uncertain significance (Nov 14, 2023)
17-31295222-T-G			Benign (Jun 12, 2018)
17-31295266-G-C		not specified	Uncertain significance (Sep 12, 2023)
17-31295295-T-C		not specified	Uncertain significance (Jan 20, 2023)
17-31295326-C-T		not specified	Uncertain significance (Sep 20, 2023)
17-31295335-G-A		not specified	Uncertain significance (Aug 16, 2021)
17-31295761-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-31295816-C-T		OMG-related disorder	Likely benign (Dec 28, 2020)
17-31295887-C-T		not specified	Uncertain significance (Oct 12, 2022)
17-31295983-A-C		not specified	Uncertain significance (Dec 11, 2023)
17-31296020-C-T		not specified	Uncertain significance (Mar 01, 2023)
17-31296054-A-G		not specified	Uncertain significance (Jul 19, 2023)
17-31296181-A-G		not specified	Uncertain significance (Aug 01, 2023)
17-31296270-C-T		OMG-related disorder	Benign (Oct 21, 2019)
17-31297157-G-A		not specified	Benign (Feb 06, 2024)
17-31297359-T-G		Hereditary cancer-predisposing syndrome	Benign (Jul 31, 2020)

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