OR5H1

olfactory receptor family 5 subfamily H member 1, the group of Olfactory receptors, family 5

Basic information

Region (hg38): 3:98130721-98138548

Links

ENSG00000231192 ∙ NCBI:26341 ∙ ∙ HGNC:8346 ∙ Uniprot:A6NKK0 ∙ 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 OR5H1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR5H1 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in OR5H1

This is a list of pathogenic ClinVar variants found in the OR5H1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98132743-G-C		not specified	Uncertain significance (Jun 10, 2024)
3-98132752-T-C		not specified	Uncertain significance (Nov 10, 2022)
3-98132810-C-T		not specified	Uncertain significance (Oct 05, 2023)
3-98132865-T-G		not specified	Uncertain significance (Mar 07, 2024)
3-98132876-A-T		not specified	Uncertain significance (May 02, 2024)
3-98132969-T-C		not specified	Uncertain significance (May 20, 2024)
3-98133000-T-G		not specified	Uncertain significance (Feb 15, 2023)
3-98133003-T-G		not specified	Uncertain significance (Nov 22, 2023)
3-98133013-A-G		not specified	Uncertain significance (Aug 28, 2021)
3-98133047-C-T		not specified	Uncertain significance (Oct 25, 2022)
3-98133095-C-G		not specified	Uncertain significance (May 28, 2023)
3-98133232-T-C		not specified	Uncertain significance (Jun 11, 2024)
3-98133308-G-T		not specified	Uncertain significance (May 17, 2023)
3-98133343-G-A		not specified	Uncertain significance (Oct 20, 2023)
3-98133350-A-G		not specified	Uncertain significance (Dec 17, 2023)
3-98133367-G-T		not specified	Uncertain significance (Mar 15, 2024)
3-98133381-G-T		not specified	Uncertain significance (Mar 01, 2024)
3-98133390-T-A		not specified	Uncertain significance (Sep 01, 2021)
3-98133439-G-T		not specified	Uncertain significance (Oct 03, 2022)
3-98133443-C-G		not specified	Uncertain significance (Jul 20, 2021)
3-98133457-C-T		not specified	Uncertain significance (Jan 31, 2023)
3-98133468-C-A		not specified	Uncertain significance (Jul 20, 2021)
3-98133471-T-G		not specified	Likely benign (Jul 20, 2021)
3-98133473-A-G		not specified	Uncertain significance (Jan 26, 2022)
3-98133490-C-T		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR5H1	protein_coding	protein_coding	ENST00000354565	1	942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000469	0.252	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.24	237	158	1.50	0.00000720	2018
Missense in Polyphen		49	34.473	1.4214		491
Synonymous	-2.08	80	59.6	1.34	0.00000292	621
Loss of Function	-0.395	6	5.04	1.19	2.09e-7	81

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: 0.849
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.8

Haploinsufficiency Scores

• pHI: 0.0930
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

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;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