OR56A1

olfactory receptor family 56 subfamily A member 1, the group of Olfactory receptors, family 56

Basic information

Region (hg38): 11:6019335-6034338

Links

ENSG00000180934 ∙ NCBI:120796 ∙ ∙ HGNC:14781 ∙ Uniprot:Q8NGH5 ∙ 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 OR56A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR56A1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in OR56A1

This is a list of pathogenic ClinVar variants found in the OR56A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6026784-T-G		not specified	Uncertain significance (Nov 27, 2023)
11-6026804-C-G		not specified	Uncertain significance (Aug 13, 2021)
11-6026809-T-G		not specified	Uncertain significance (Apr 05, 2023)
11-6026986-G-A		not specified	Uncertain significance (Oct 27, 2022)
11-6027005-T-C		not specified	Uncertain significance (Mar 07, 2024)
11-6027095-T-G		not specified	Likely benign (Sep 26, 2023)
11-6027097-C-T		not specified	Uncertain significance (Aug 02, 2021)
11-6027142-T-G		not specified	Uncertain significance (Jan 19, 2024)
11-6027178-C-T		not specified	Uncertain significance (Apr 07, 2022)
11-6027233-G-A		not specified	Uncertain significance (Jun 11, 2024)
11-6027260-C-A		not specified	Uncertain significance (Jan 24, 2023)
11-6027343-G-A		not specified	Uncertain significance (Jan 10, 2022)
11-6027386-G-T		not specified	Uncertain significance (Apr 13, 2023)
11-6027389-G-A		not specified	Likely benign (Dec 14, 2022)
11-6027449-G-A		not specified	Uncertain significance (Oct 22, 2021)
11-6027455-C-T		not specified	Uncertain significance (Jun 11, 2024)
11-6027472-A-G		not specified	Uncertain significance (Sep 16, 2021)
11-6027506-A-C		not specified	Uncertain significance (Apr 07, 2022)
11-6027553-G-T		not specified	Uncertain significance (Jan 08, 2024)
11-6027626-A-G		not specified	Uncertain significance (Mar 29, 2023)
11-6027668-T-C		not specified	Uncertain significance (Jun 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR56A1	protein_coding	protein_coding	ENST00000316650	1	1071

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000560	0.484	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.327	187	175	1.07	0.00000885	2072
Missense in Polyphen		47	56.943	0.82539		752
Synonymous	-1.05	87	75.4	1.15	0.00000403	680
Loss of Function	0.204	5	5.52	0.906	2.33e-7	70

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: 0.0882

Intolerance Scores

• loftool: 0.510
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.146
• ghis: 0.435

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00641

Gene Damage Prediction

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

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