OR1L4

olfactory receptor family 1 subfamily L member 4, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 9:122723990-122724925

Previous symbols: [ "OR1L5" ]

Links

ENSG00000136939 ∙ NCBI:254973 ∙ ∙ HGNC:8216 ∙ Uniprot:Q8NGR5 ∙ 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 OR1L4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1L4 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in OR1L4

This is a list of pathogenic ClinVar variants found in the OR1L4 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-122724024-G-A		not specified	Uncertain significance (May 18, 2022)
9-122724039-G-C		not specified	Uncertain significance (Apr 09, 2024)
9-122724110-G-T		not specified	Uncertain significance (Aug 30, 2022)
9-122724155-C-T		not specified	Uncertain significance (May 20, 2024)
9-122724184-C-A		not specified	Uncertain significance (Nov 08, 2022)
9-122724198-T-C		not specified	Uncertain significance (Aug 31, 2022)
9-122724223-A-G		not specified	Uncertain significance (Apr 05, 2023)
9-122724251-T-A		not specified	Uncertain significance (Oct 16, 2023)
9-122724254-G-A		not specified	Uncertain significance (Jun 12, 2023)
9-122724266-A-C		not specified	Uncertain significance (Dec 21, 2023)
9-122724275-G-A		not specified	Uncertain significance (Nov 17, 2022)
9-122724311-T-C		not specified	Uncertain significance (Aug 02, 2021)
9-122724353-G-A		not specified	Uncertain significance (Nov 13, 2023)
9-122724365-G-A		not specified	Uncertain significance (Mar 03, 2022)
9-122724392-G-A		not specified	Uncertain significance (Dec 15, 2021)
9-122724431-G-T		not specified	Uncertain significance (Jan 24, 2023)
9-122724447-C-G		not specified	Uncertain significance (Dec 30, 2023)
9-122724467-C-T		not specified	Uncertain significance (Mar 16, 2023)
9-122724468-G-A		not specified	Uncertain significance (May 31, 2023)
9-122724481-G-A		not specified	Uncertain significance (Dec 12, 2023)
9-122724491-T-C		not specified	Uncertain significance (Jul 05, 2023)
9-122724507-A-G		not specified	Uncertain significance (Sep 29, 2022)
9-122724531-A-G		not specified	Uncertain significance (Mar 15, 2024)
9-122724608-G-A		not specified	Uncertain significance (Oct 03, 2022)
9-122724759-T-C		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1L4	protein_coding	protein_coding	ENST00000259466	1	936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000316	0.205	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.712	182	157	1.16	0.00000790	2008
Missense in Polyphen		69	57.426	1.2015		773
Synonymous	-0.749	72	64.4	1.12	0.00000321	636
Loss of Function	-0.634	6	4.54	1.32	1.96e-7	73

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: 0.0761

Intolerance Scores

• loftool: 0.615
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.25

Haploinsufficiency Scores

• pHI: 0.274
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr365

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