OR3A3

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

Basic information

Region (hg38): 17:3411370-3424070

Previous symbols: [ "OR3A6", "OR3A7", "OR3A8P" ]

Links

ENSG00000159961 ∙ NCBI:8392 ∙ ∙ HGNC:8284 ∙ Uniprot:P47888 ∙ 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 OR3A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR3A3 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			15	3		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	15	3	0

Variants in OR3A3

This is a list of pathogenic ClinVar variants found in the OR3A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3420625-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-3420739-G-A		not specified	Likely benign (Sep 27, 2022)
17-3420745-G-A		not specified	Uncertain significance (Apr 12, 2022)
17-3420764-C-T		not specified	Uncertain significance (Feb 28, 2023)
17-3420771-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-3420869-T-C		not specified	Uncertain significance (Dec 20, 2023)
17-3420916-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-3420953-A-G		not specified	Uncertain significance (Sep 14, 2023)
17-3420959-G-A		not specified	Uncertain significance (Apr 29, 2024)
17-3420986-C-A		not specified	Uncertain significance (Jan 26, 2022)
17-3420998-G-A		not specified	Uncertain significance (Dec 15, 2022)
17-3421109-A-G		not specified	Likely benign (Sep 14, 2021)
17-3421119-T-A		not specified	Uncertain significance (Nov 08, 2022)
17-3421153-C-T		not specified	Uncertain significance (Aug 23, 2021)
17-3421228-G-A		not specified	Uncertain significance (Oct 29, 2021)
17-3421238-G-A		not specified	Uncertain significance (Nov 08, 2021)
17-3421279-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-3421280-G-A		not specified	Likely benign (Nov 12, 2021)
17-3421471-A-G		not specified	Uncertain significance (Aug 03, 2022)
17-3421472-G-A		not specified	Uncertain significance (May 02, 2024)
17-3421492-G-A		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR3A3	protein_coding	protein_coding	ENST00000291231	1	966

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000171	0.277	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	143	163	0.875	0.00000849	2068
Missense in Polyphen		23	36.279	0.63397		564
Synonymous	0.953	60	70.1	0.855	0.00000388	701
Loss of Function	-0.545	5	3.85	1.30	2.46e-7	46

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);GPCRs, Other;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)

Recessive Scores

• pRec: 0.0845

Intolerance Scores

• loftool: 0.813
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.58

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255
• ghis: 0.412

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0712

Gene Damage Prediction

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

Gene ontology

• Biological process: signal transduction;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