OR56A4

olfactory receptor family 56 subfamily A member 4, the group of Olfactory receptors, family 56

Basic information

Region (hg38): 11:5999444-6006946

Links

ENSG00000183389 ∙ NCBI:120793 ∙ ∙ HGNC:14791 ∙ Uniprot:Q8NGH8 ∙ 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 OR56A4 gene.

• Inborn genetic diseases (25 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR56A4 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	2		4
Total	0	0	22	3	0

Variants in OR56A4

This is a list of pathogenic ClinVar variants found in the OR56A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6002076-A-G		not specified	Uncertain significance (Jan 04, 2024)
11-6002140-G-C		not specified	Uncertain significance (Aug 26, 2022)
11-6002245-G-C		not specified	Uncertain significance (Jun 03, 2022)
11-6002269-T-C		not specified	Uncertain significance (Jun 29, 2023)
11-6002274-G-A		not specified	Uncertain significance (Jan 17, 2024)
11-6002295-G-T		not specified	Uncertain significance (Jun 02, 2023)
11-6002400-T-C		not specified	Uncertain significance (Mar 29, 2023)
11-6002419-A-T		not specified	Uncertain significance (Feb 28, 2023)
11-6002451-A-T		not specified	Uncertain significance (Aug 08, 2022)
11-6002514-A-T		not specified	Uncertain significance (Jun 03, 2022)
11-6002533-G-A		not specified	Uncertain significance (Apr 08, 2022)
11-6002538-A-G		not specified	Uncertain significance (Aug 21, 2023)
11-6002551-C-A		not specified	Uncertain significance (Aug 12, 2021)
11-6002678-G-T		not specified	Uncertain significance (Jul 26, 2022)
11-6002694-C-A		not specified	Uncertain significance (Dec 01, 2022)
11-6002698-C-A		not specified	Uncertain significance (Mar 07, 2024)
11-6002712-G-C		not specified	Uncertain significance (Apr 12, 2023)
11-6002721-T-G		not specified	Uncertain significance (Sep 27, 2021)
11-6002755-C-T		not specified	Uncertain significance (Apr 05, 2023)
11-6002771-G-C		not specified	Uncertain significance (Aug 04, 2023)
11-6002829-T-G		not specified	Uncertain significance (Apr 13, 2022)
11-6002841-G-T		not specified	Uncertain significance (Feb 21, 2024)
11-6002850-A-T		not specified	Uncertain significance (Feb 15, 2023)
11-6002857-T-G		not specified	Uncertain significance (Jan 23, 2024)
11-6002895-G-A		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR56A4	protein_coding	protein_coding	ENST00000330728	1	1209

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00841	0.809	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.423	212	195	1.09	0.00000931	2386
Missense in Polyphen		44	48.298	0.91101		663
Synonymous	-1.85	104	82.6	1.26	0.00000434	772
Loss of Function	1.04	4	6.98	0.573	2.94e-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)

Intolerance Scores

• loftool: 0.745
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.233
• hipred: N
• hipred_score: 0.146
• ghis: 0.429

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0121

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr684

Gene ontology

• Biological process: synaptic transmission, dopaminergic;adenylate cyclase-modulating G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting dopamine receptor signaling pathway;regulation of dopamine secretion;response to drug;behavioral response to cocaine;detection of chemical stimulus involved in sensory perception of smell;adenylate cyclase-activating adrenergic receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: dopamine neurotransmitter receptor activity, coupled via Gi/Go;adrenergic receptor activity;olfactory receptor activity;dopamine binding