OR4N2

olfactory receptor family 4 subfamily N member 2, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 14:19719015-19830253

Links

ENSG00000176294 ∙ NCBI:390429 ∙ ∙ HGNC:14742 ∙ Uniprot:Q8NGD1 ∙ 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 OR4N2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4N2 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in OR4N2

This is a list of pathogenic ClinVar variants found in the OR4N2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-19747482-T-A		not specified	Uncertain significance (Mar 31, 2023)
14-19747546-T-C		not specified	Uncertain significance (Jun 29, 2022)
14-19747560-A-T		not specified	Uncertain significance (Jan 22, 2024)
14-19747581-C-T		not specified	Uncertain significance (May 27, 2022)
14-19747662-G-C		not specified	Uncertain significance (Nov 08, 2022)
14-19747665-C-T		not specified	Uncertain significance (Jan 19, 2022)
14-19747669-A-T		not specified	Uncertain significance (May 20, 2024)
14-19747673-G-A		not specified	Uncertain significance (Jan 27, 2022)
14-19747750-T-C		not specified	Uncertain significance (May 14, 2024)
14-19747770-T-C			Likely benign (Jul 01, 2022)
14-19747785-G-T		not specified	Uncertain significance (Jan 05, 2022)
14-19747821-C-T		not specified	Uncertain significance (Jan 23, 2024)
14-19747896-T-G		not specified	Uncertain significance (Apr 17, 2023)
14-19747899-A-G		not specified	Uncertain significance (Dec 09, 2023)
14-19747911-A-G		not specified	Uncertain significance (Apr 22, 2022)
14-19747915-T-A		not specified	Uncertain significance (Jun 06, 2023)
14-19747955-C-A		not specified	Uncertain significance (Aug 02, 2022)
14-19748000-G-A		not specified	Uncertain significance (Jan 24, 2024)
14-19748019-G-T		not specified	Uncertain significance (Jun 17, 2024)
14-19748048-G-C			Likely benign (Aug 01, 2022)
14-19748079-T-G		not specified	Uncertain significance (Sep 26, 2023)
14-19748088-A-G		not specified	Likely benign (Dec 21, 2023)
14-19748104-T-G		not specified	Uncertain significance (Mar 07, 2024)
14-19748130-A-G		not specified	Uncertain significance (Oct 30, 2023)
14-19748184-G-A		not specified	Likely benign (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4N2	protein_coding	protein_coding	ENST00000315947	1	109358

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000411	0.422	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.19	232	155	1.49	0.00000843	1951
Missense in Polyphen		60	44.921	1.3357		662
Synonymous	-2.22	79	57.6	1.37	0.00000302	607
Loss of Function	0.0227	5	5.05	0.989	3.17e-7	69

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)

Recessive Scores

• pRec: 0.0886

Intolerance Scores

• loftool: 0.680
• rvis_EVS: 2.26
• rvis_percentile_EVS: 98.22

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

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