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.

• not_specified (48 variants)

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. These statistics are base on transcript: NM_001004059.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			47	1		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	1	0

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