OR4A16

olfactory receptor family 4 subfamily A member 16, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:55343200-55344187

Links

ENSG00000181961 ∙ NCBI:81327 ∙ ∙ HGNC:15153 ∙ Uniprot:Q8NH70 ∙ 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 OR4A16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4A16 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			21	4		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	21	4	0

Variants in OR4A16

This is a list of pathogenic ClinVar variants found in the OR4A16 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-55343211-G-A		not specified	Likely benign (May 16, 2022)
11-55343213-A-T		not specified	Uncertain significance (Jun 18, 2021)
11-55343219-G-A		not specified	Likely benign (Jul 05, 2023)
11-55343399-A-G		not specified	Uncertain significance (Mar 31, 2024)
11-55343405-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-55343415-C-A		not specified	Uncertain significance (Oct 25, 2022)
11-55343421-C-T		not specified	Uncertain significance (Mar 07, 2024)
11-55343423-A-T		not specified	Uncertain significance (Jan 23, 2024)
11-55343480-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-55343488-G-A		not specified	Uncertain significance (May 11, 2022)
11-55343573-T-C		not specified	Uncertain significance (Sep 06, 2022)
11-55343587-C-G		not specified	Uncertain significance (Dec 16, 2021)
11-55343598-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-55343649-G-T		not specified	Uncertain significance (Dec 02, 2022)
11-55343666-G-A		not specified	Uncertain significance (Oct 22, 2021)
11-55343690-C-A		not specified	Uncertain significance (May 05, 2023)
11-55343711-G-A		not specified	Uncertain significance (Dec 02, 2022)
11-55343777-A-G		not specified	Uncertain significance (May 20, 2024)
11-55343778-T-C		not specified	Uncertain significance (Apr 09, 2024)
11-55343783-C-A		not specified	Uncertain significance (Jul 20, 2021)
11-55343796-C-T		not specified	Likely benign (May 05, 2023)
11-55343799-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-55343820-T-C		not specified	Uncertain significance (Mar 16, 2022)
11-55343844-C-T		not specified	Uncertain significance (May 01, 2022)
11-55343884-G-T		not specified	Uncertain significance (May 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4A16	protein_coding	protein_coding	ENST00000314721	1	1081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000228	0.319	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.68	300	166	1.80	0.00000786	2105
Missense in Polyphen		57	39.102	1.4577		599
Synonymous	-4.50	106	61.2	1.73	0.00000302	645
Loss of Function	-0.349	5	4.23	1.18	2.47e-7	65

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)

Intolerance Scores

• loftool: 0.945
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.173

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr1240

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