OR1J1

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

Basic information

Region (hg38): 9:122476958-122477926

Links

ENSG00000136834 ∙ NCBI:347168 ∙ ∙ HGNC:8208 ∙ Uniprot:Q8NGS3 ∙ 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 OR1J1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1J1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in OR1J1

This is a list of pathogenic ClinVar variants found in the OR1J1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-122476983-C-G		not specified	Uncertain significance (Apr 08, 2024)
9-122476999-C-T		not specified	Uncertain significance (Apr 22, 2022)
9-122477013-A-G		not specified	Uncertain significance (Dec 15, 2023)
9-122477107-C-T		not specified	Uncertain significance (Aug 21, 2023)
9-122477112-A-G		not specified	Uncertain significance (Dec 05, 2024)
9-122477113-T-C		not specified	Uncertain significance (May 17, 2023)
9-122477128-T-G		not specified	Uncertain significance (Dec 13, 2023)
9-122477130-T-C		not specified	Uncertain significance (Aug 15, 2023)
9-122477161-T-C		not specified	Uncertain significance (Mar 29, 2024)
9-122477185-C-T		not specified	Uncertain significance (Mar 20, 2024)
9-122477227-T-G		not specified	Uncertain significance (Jan 24, 2023)
9-122477289-C-T		not specified	Uncertain significance (Jun 29, 2023)
9-122477354-G-T		not specified	Uncertain significance (Jan 22, 2024)
9-122477395-A-G		not specified	Uncertain significance (Mar 01, 2023)
9-122477430-A-T		not specified	Uncertain significance (Aug 05, 2023)
9-122477433-T-C		not specified	Likely benign (Sep 22, 2023)
9-122477474-G-C		not specified	Uncertain significance (Sep 08, 2024)
9-122477521-T-C		not specified	Uncertain significance (Jan 04, 2024)
9-122477715-A-T		not specified	Uncertain significance (May 11, 2022)
9-122477728-C-T		not specified	Uncertain significance (Nov 11, 2024)
9-122477802-T-A		not specified	Uncertain significance (Jun 17, 2024)
9-122477838-A-T		not specified	Uncertain significance (Feb 16, 2023)
9-122477842-C-T		not specified	Uncertain significance (Dec 14, 2023)
9-122477863-C-G		not specified	Uncertain significance (Jun 11, 2021)
9-122477870-G-C		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1J1	protein_coding	protein_coding	ENST00000259357	1	1016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000683	0.305	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.552	196	175	1.12	0.00000864	2097
Missense in Polyphen		51	50.743	1.0051		693
Synonymous	-0.407	78	73.6	1.06	0.00000396	680
Loss of Function	-0.182	6	5.54	1.08	2.33e-7	82

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: 0.0821

Intolerance Scores

• loftool: 0.704
• rvis_EVS: 1.31
• rvis_percentile_EVS: 94

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr3

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