OR4S2

olfactory receptor family 4 subfamily S member 2, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:55648327-55652854

Previous symbols: [ "OR4S2P" ]

Links

ENSG00000174982 ∙ NCBI:219431 ∙ ∙ HGNC:15183 ∙ Uniprot:Q8NH73 ∙ 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 OR4S2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4S2 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in OR4S2

This is a list of pathogenic ClinVar variants found in the OR4S2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-55650917-A-C		not specified	Uncertain significance (Dec 05, 2024)
11-55650920-A-G		not specified	Uncertain significance (Jun 29, 2022)
11-55650930-A-T		not specified	Uncertain significance (Jun 16, 2024)
11-55650946-C-A		not specified	Uncertain significance (Dec 21, 2022)
11-55651032-C-G		not specified	Uncertain significance (Mar 21, 2023)
11-55651073-T-C		not specified	Uncertain significance (Jul 19, 2023)
11-55651129-G-C		not specified	Uncertain significance (Oct 03, 2023)
11-55651135-A-G		not specified	Uncertain significance (Jul 14, 2021)
11-55651169-C-G		not specified	Uncertain significance (Nov 09, 2024)
11-55651189-A-C		not specified	Uncertain significance (Oct 02, 2023)
11-55651197-A-C		not specified	Uncertain significance (Feb 17, 2024)
11-55651219-G-T		not specified	Uncertain significance (Apr 07, 2022)
11-55651262-G-A		not specified	Uncertain significance (Jan 23, 2023)
11-55651265-A-T		not specified	Uncertain significance (Aug 01, 2024)
11-55651276-T-C		not specified	Uncertain significance (Oct 20, 2023)
11-55651283-C-A		not specified	Uncertain significance (Nov 04, 2023)
11-55651283-C-T		not specified	Uncertain significance (May 13, 2024)
11-55651310-G-A		not specified	Likely benign (Apr 23, 2024)
11-55651340-C-T		not specified	Uncertain significance (Jul 26, 2024)
11-55651364-C-A		not specified	Uncertain significance (Feb 06, 2023)
11-55651378-G-A		not specified	Uncertain significance (May 06, 2022)
11-55651394-T-C		not specified	Uncertain significance (Jun 24, 2022)
11-55651412-A-G		not specified	Uncertain significance (Jan 23, 2024)
11-55651424-A-T		not specified	Uncertain significance (Nov 21, 2024)
11-55651427-A-C		not specified	Uncertain significance (Nov 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4S2	protein_coding	protein_coding	ENST00000312422	1	936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-10	0.00854	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.173	174	168	1.04	0.00000810	2041
Missense in Polyphen		46	48.734	0.9439		638
Synonymous	1.68	45	61.8	0.729	0.00000303	617
Loss of Function	-2.24	11	5.39	2.04	2.23e-7	89

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: 0.0953

Intolerance Scores

• loftool: 0.912
• rvis_EVS: 2.04
• rvis_percentile_EVS: 97.74

Haploinsufficiency Scores

• pHI: 0.159
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1193

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