OR1S2

olfactory receptor family 1 subfamily S member 2, the group of Olfactory receptors, family 1

Basic information

Region (hg38): 11:58203204-58204142

Links

ENSG00000197887 ∙ NCBI:219958 ∙ ∙ HGNC:15141 ∙ Uniprot:Q8NGQ3 ∙ 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 OR1S2 gene.

• not_specified (55 variants)
• not_provided (5 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR1S2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001004459.2. 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				5		5
missense			52	3		55
nonsense						0
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	8	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR1S2	protein_coding	protein_coding	ENST00000302592	1	980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000872	0.186	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.61	223	165	1.35	0.00000808	2128
Missense in Polyphen		72	55.459	1.2982		749
Synonymous	-2.18	87	64.7	1.35	0.00000328	658
Loss of Function	-0.479	7	5.76	1.22	2.47e-7	80

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: 0.0818

Intolerance Scores

• loftool: 0.823
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0592

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1496

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