OMP

olfactory marker protein

Basic information

Region (hg38): 11:77102840-77103331

Links

ENSG00000254550 ∙ NCBI:4975 ∙ OMIM:164340 ∙ HGNC:8136 ∙ Uniprot:P47874 ∙ 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 OMP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OMP 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
missense			16	1		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	16	2	0

Variants in OMP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-77102885-G-C		not specified	Uncertain significance (May 30, 2024)
11-77102916-G-T		not specified	Uncertain significance (Feb 21, 2024)
11-77102917-G-A			Likely benign (Jan 01, 2024)
11-77102924-G-A		not specified	Likely benign (Dec 27, 2023)
11-77102942-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-77102954-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-77102955-G-A		not specified	Uncertain significance (Mar 30, 2024)
11-77103023-C-T		not specified	Uncertain significance (Aug 08, 2022)
11-77103033-T-C		not specified	Uncertain significance (Jun 01, 2023)
11-77103035-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-77103038-C-T		not specified	Uncertain significance (Oct 28, 2023)
11-77103097-C-G		not specified	Uncertain significance (Oct 17, 2023)
11-77103108-A-C		not specified	Uncertain significance (Jun 22, 2021)
11-77103110-C-T		not specified	Uncertain significance (Dec 05, 2022)
11-77103128-C-T		not specified	Uncertain significance (May 24, 2023)
11-77103161-C-T		not specified	Uncertain significance (Dec 17, 2023)
11-77103266-G-A		not specified	Likely benign (Mar 18, 2024)
11-77103266-G-T		not specified	Uncertain significance (Dec 19, 2022)
11-77103311-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-77103327-T-C		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OMP	protein_coding	protein_coding	ENST00000529803	1	492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000405	0.420	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.168	118	113	1.04	0.00000819	1058
Missense in Polyphen		42	42.049	0.99883		450
Synonymous	0.825	44	51.5	0.854	0.00000375	339
Loss of Function	0.0137	5	5.03	0.993	2.19e-7	47

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a modulator of the olfactory signal- transduction cascade.

Intolerance Scores

• loftool: 0.486
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.231
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Omp
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; craniofacial phenotype; taste/olfaction phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype

Gene ontology

• Biological process: signal transduction;chemical synaptic transmission;sensory perception of smell;neurogenesis
• Cellular component: nucleus;cytosol;axon;neuronal cell body