OR1N2

olfactory receptor family 1 subfamily N member 2, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 9:122553112-122554214

Links

ENSG00000171501 ∙ NCBI:138882 ∙ ∙ HGNC:15111 ∙ Uniprot:Q8NGR9 ∙ 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 OR1N2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1N2 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			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	0	1

Variants in OR1N2

This is a list of pathogenic ClinVar variants found in the OR1N2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-122553287-G-A		not specified	Uncertain significance (Jun 12, 2023)
9-122553380-C-T		not specified	Uncertain significance (May 11, 2022)
9-122553461-A-T		not specified	Uncertain significance (Jan 27, 2022)
9-122553498-C-T		not specified	Uncertain significance (Jul 11, 2023)
9-122553579-A-G		not specified	Uncertain significance (Jun 24, 2022)
9-122553584-C-T			Benign (May 24, 2018)
9-122553633-C-T		not specified	Uncertain significance (May 12, 2024)
9-122553714-G-A		not specified	Uncertain significance (Aug 28, 2023)
9-122553716-G-A		not specified	Uncertain significance (Aug 11, 2022)
9-122553727-T-G		not specified	Uncertain significance (Aug 14, 2023)
9-122553747-A-G		not specified	Uncertain significance (Sep 29, 2022)
9-122553752-T-C		not specified	Uncertain significance (Feb 10, 2023)
9-122553753-A-C		not specified	Uncertain significance (Apr 26, 2023)
9-122553777-A-G		not specified	Uncertain significance (Sep 14, 2021)
9-122553779-C-T		not specified	Uncertain significance (Jun 17, 2024)
9-122553780-T-C		not specified	Uncertain significance (Jul 13, 2022)
9-122553936-C-A		not specified	Uncertain significance (Feb 06, 2023)
9-122553978-G-T		not specified	Uncertain significance (May 02, 2024)
9-122554057-G-A		not specified	Uncertain significance (Oct 17, 2023)
9-122554073-C-G		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1N2	protein_coding	protein_coding	ENST00000373688	1	1103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000149	0.247	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.132	167	172	0.972	0.00000855	2131
Missense in Polyphen		57	59.366	0.96015		763
Synonymous	-0.540	75	69.3	1.08	0.00000352	703
Loss of Function	-0.209	7	6.43	1.09	2.79e-7	90

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: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 0.86
• rvis_percentile_EVS: 88.74

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0610

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr354

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity