OR5AP2

olfactory receptor family 5 subfamily AP member 2, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 11:56641489-56642439

Links

ENSG00000172464 ∙ NCBI:338675 ∙ ∙ HGNC:15258 ∙ Uniprot:Q8NGF4 ∙ 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 OR5AP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5AP2 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in OR5AP2

This is a list of pathogenic ClinVar variants found in the OR5AP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-56641499-T-C		not specified	Uncertain significance (Jun 21, 2021)
11-56641500-G-A		not specified	Uncertain significance (Feb 22, 2023)
11-56641545-T-G		not specified	Uncertain significance (Jan 05, 2022)
11-56641605-C-T		not specified	Likely benign (Jul 27, 2024)
11-56641640-C-T		not specified	Uncertain significance (Apr 25, 2022)
11-56641651-G-T		not specified	Uncertain significance (Jan 03, 2024)
11-56641692-A-C		not specified	Uncertain significance (May 01, 2022)
11-56641698-C-T		not specified	Uncertain significance (Nov 09, 2021)
11-56641706-G-C		not specified	Uncertain significance (Jan 24, 2024)
11-56641733-G-A			Likely benign (Jan 01, 2023)
11-56641824-T-G		not specified	Uncertain significance (Sep 13, 2023)
11-56641902-T-A		not specified	Uncertain significance (May 27, 2022)
11-56641911-A-G		not specified	Uncertain significance (Jun 26, 2024)
11-56641956-C-T		not specified	Uncertain significance (Jan 19, 2022)
11-56641968-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-56641987-T-C		not specified	Uncertain significance (Jan 30, 2024)
11-56641989-T-C		not specified	Likely benign (Mar 29, 2023)
11-56642016-C-T		not specified	Likely benign (Oct 26, 2024)
11-56642066-G-A		not specified	Uncertain significance (Oct 06, 2021)
11-56642102-A-C		not specified	Uncertain significance (Dec 03, 2021)
11-56642193-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-56642265-G-T		not specified	Uncertain significance (Dec 14, 2023)
11-56642307-T-G		not specified	Uncertain significance (Sep 01, 2021)
11-56642343-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-56642364-T-G		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5AP2	protein_coding	protein_coding	ENST00000302981	1	1006

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00416	0.674	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0462	169	167	1.01	0.00000796	2089
Missense in Polyphen		55	56.734	0.96943		785
Synonymous	-0.117	66	64.8	1.02	0.00000324	629
Loss of Function	0.620	4	5.58	0.717	2.97e-7	85

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: 0.0973

Intolerance Scores

• loftool: 0.624
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.63

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0268

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1020

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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;odorant binding