OR4D9

olfactory receptor family 4 subfamily D member 9, the group of Olfactory receptors, family 4

Basic information

Region (hg38): 11:59511368-59520703

Links

ENSG00000172742 ∙ NCBI:390199 ∙ ∙ HGNC:15178 ∙ Uniprot:Q8NGE8 ∙ 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 OR4D9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR4D9 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	1		20
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	1	0

Variants in OR4D9

This is a list of pathogenic ClinVar variants found in the OR4D9 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-59514971-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-59515015-T-C		not specified	Uncertain significance (Oct 16, 2024)
11-59515018-A-G		not specified	Uncertain significance (May 05, 2023)
11-59515075-C-A		not specified	Uncertain significance (May 31, 2023)
11-59515087-A-G		not specified	Uncertain significance (Jun 28, 2022)
11-59515162-G-C		not specified	Uncertain significance (Jul 31, 2024)
11-59515178-C-A		not specified	Uncertain significance (Apr 13, 2022)
11-59515234-G-T		not specified	Uncertain significance (May 17, 2023)
11-59515238-G-T		not specified	Uncertain significance (Dec 11, 2023)
11-59515246-G-T		not specified	Uncertain significance (Nov 03, 2022)
11-59515283-T-C		not specified	Uncertain significance (Jan 04, 2022)
11-59515300-C-G		not specified	Uncertain significance (Aug 02, 2022)
11-59515312-A-G		not specified	Uncertain significance (Jul 05, 2023)
11-59515348-G-A		not specified	Uncertain significance (Sep 08, 2024)
11-59515443-C-G		not specified	Uncertain significance (Jan 19, 2024)
11-59515514-C-T		not specified	Uncertain significance (Jan 23, 2024)
11-59515673-G-C			Likely benign (Feb 01, 2023)
11-59515687-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-59515690-C-T		not specified	Uncertain significance (Oct 16, 2024)
11-59515706-T-C		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR4D9	protein_coding	protein_coding	ENST00000329328	1	945

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000961	0.599	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.930	207	173	1.20	0.00000904	2044
Missense in Polyphen		63	42.147	1.4948		591
Synonymous	-0.801	79	70.4	1.12	0.00000392	672
Loss of Function	0.510	5	6.39	0.782	4.41e-7	68

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: 0.885
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.28

Haploinsufficiency Scores

• pHI: 0.0354
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0659

Gene Damage Prediction

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

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