OR1L3

olfactory receptor family 1 subfamily L member 3, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 9:122675130-122676104

Links

ENSG00000171481 ∙ NCBI:26735 ∙ ∙ HGNC:8215 ∙ Uniprot:Q8NH93 ∙ 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 OR1L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1L3 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			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in OR1L3

This is a list of pathogenic ClinVar variants found in the OR1L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-122675217-C-T		not specified	Uncertain significance (Oct 13, 2021)
9-122675264-C-G		not specified	Uncertain significance (Feb 07, 2023)
9-122675319-A-C		not specified	Uncertain significance (Dec 17, 2023)
9-122675328-T-C		not specified	Uncertain significance (Dec 20, 2023)
9-122675353-C-G		not specified	Uncertain significance (May 21, 2024)
9-122675359-T-C		not specified	Uncertain significance (Feb 09, 2023)
9-122675457-A-G		not specified	Uncertain significance (Jan 16, 2024)
9-122675476-C-T		not specified	Uncertain significance (Nov 09, 2023)
9-122675536-T-C		not specified	Uncertain significance (Sep 20, 2023)
9-122675638-C-T		not specified	Uncertain significance (Jul 06, 2021)
9-122675737-G-T		not specified	Uncertain significance (Jan 04, 2022)
9-122675770-T-C		not specified	Uncertain significance (Nov 15, 2023)
9-122675778-T-G		not specified	Uncertain significance (Jan 06, 2023)
9-122675799-G-A		not specified	Likely benign (Jun 21, 2023)
9-122675844-T-C		not specified	Uncertain significance (May 04, 2022)
9-122675941-G-A		not specified	Uncertain significance (Jan 16, 2024)
9-122676017-G-A		not specified	Uncertain significance (Mar 07, 2023)
9-122676021-C-T		not specified	Uncertain significance (Jan 06, 2023)
9-122676090-A-G		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1L3	protein_coding	protein_coding	ENST00000304820	1	1118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000176	0.280	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.557	188	168	1.12	0.00000843	2113
Missense in Polyphen		51	39.896	1.2783		613
Synonymous	0.842	55	63.5	0.866	0.00000294	668
Loss of Function	-0.527	5	3.88	1.29	2.07e-7	66

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: 0.833
• rvis_EVS: 2.31
• rvis_percentile_EVS: 98.34

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

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