OR2J2

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

Basic information

Region (hg38): 6:29170907-29175811

Links

ENSG00000204700 ∙ NCBI:26707 ∙ ∙ HGNC:8260 ∙ Uniprot:O76002 ∙ 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 OR2J2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2J2 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in OR2J2

This is a list of pathogenic ClinVar variants found in the OR2J2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-29173652-A-G		not specified	Uncertain significance (Apr 20, 2024)
6-29173679-T-C		not specified	Uncertain significance (Mar 11, 2022)
6-29173682-T-C		not specified	Uncertain significance (Jun 23, 2023)
6-29173702-C-G		not specified	Uncertain significance (Sep 21, 2021)
6-29173765-C-G		not specified	Uncertain significance (Jan 03, 2022)
6-29173853-G-C		not specified	Uncertain significance (Jul 27, 2022)
6-29173894-C-T		not specified	Likely benign (Dec 16, 2021)
6-29174054-G-A		not specified	Uncertain significance (Oct 06, 2021)
6-29174204-G-A		not specified	Uncertain significance (Nov 21, 2022)
6-29174249-C-G		not specified	Uncertain significance (Jul 14, 2021)
6-29174319-C-G		not specified	Likely benign (Aug 08, 2022)
6-29174345-A-G		not specified	Uncertain significance (Jan 26, 2022)
6-29174359-T-C		not specified	Uncertain significance (Mar 18, 2024)
6-29174363-G-A		not specified	Uncertain significance (Mar 04, 2024)
6-29174405-T-C		not specified	Uncertain significance (Oct 05, 2023)
6-29174423-C-T		not specified	Uncertain significance (Jun 13, 2024)
6-29174444-A-C		not specified	Uncertain significance (Apr 12, 2023)
6-29174486-C-T		not specified	Uncertain significance (Sep 26, 2023)
6-29174489-G-A		not specified	Uncertain significance (May 08, 2024)
6-29174534-G-T		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2J2	protein_coding	protein_coding	ENST00000377167	1	1041

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0195	0.754	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.242	180	171	1.05	0.00000889	2011
Missense in Polyphen		42	48.609	0.86403		660
Synonymous	-0.380	69	65.1	1.06	0.00000341	660
Loss of Function	0.831	3	5.01	0.599	2.11e-7	72

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;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.592
• rvis_EVS: 1.57
• rvis_percentile_EVS: 95.74

Haploinsufficiency Scores

• pHI: 0.0801
• hipred: N
• hipred_score: 0.112
• ghis: 0.394

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00258

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

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