OR13H1

olfactory receptor family 13 subfamily H member 1, the group of Olfactory receptors, family 13

Basic information

Region (hg38): X:131544073-131545000

Links

ENSG00000171054 ∙ NCBI:347468 ∙ ∙ HGNC:14755 ∙ Uniprot:Q8NG92 ∙ 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 OR13H1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR13H1 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				2	1	3
missense			22	2	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	4	3

Variants in OR13H1

This is a list of pathogenic ClinVar variants found in the OR13H1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-131544081-T-C		not specified	Uncertain significance (Jun 27, 2023)
X-131544105-A-G		not specified	Uncertain significance (Jan 31, 2023)
X-131544117-T-C		not specified	Uncertain significance (Aug 03, 2022)
X-131544117-T-G		not specified	Uncertain significance (Nov 08, 2022)
X-131544150-C-T			Likely benign (Dec 31, 2019)
X-131544234-A-G		not specified	Uncertain significance (Apr 24, 2023)
X-131544249-T-A			Benign (Mar 29, 2018)
X-131544257-T-C		not specified	Uncertain significance (Nov 03, 2023)
X-131544264-G-A		not specified	Uncertain significance (Dec 21, 2022)
X-131544299-G-C		not specified	Uncertain significance (Jan 31, 2023)
X-131544313-G-A			Benign (May 21, 2018)
X-131544347-C-T		not specified	Uncertain significance (Jul 06, 2021)
X-131544386-T-C			Likely benign (Sep 10, 2018)
X-131544413-C-T			Likely benign (Jun 01, 2018)
X-131544438-G-A		not specified	Uncertain significance (Oct 26, 2022)
X-131544527-T-C		not specified	Uncertain significance (Jun 06, 2023)
X-131544558-C-A		not specified	Uncertain significance (Jun 01, 2023)
X-131544624-T-A		not specified	Uncertain significance (Jan 31, 2024)
X-131544786-C-A		not specified	Uncertain significance (Aug 16, 2022)
X-131544806-A-C			Likely benign (Dec 01, 2022)
X-131544809-G-A		not specified	Uncertain significance (May 29, 2024)
X-131544839-T-C		not specified	Uncertain significance (Jun 06, 2023)
X-131544889-T-A		not specified	Uncertain significance (Dec 19, 2023)
X-131544891-T-A		not specified	Uncertain significance (Dec 19, 2023)
X-131544905-G-A		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR13H1	protein_coding	protein_coding	ENST00000338616	1	1081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000255	0.182	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	119	115	1.04	0.00000811	2004
Missense in Polyphen		38	35.784	1.0619		680
Synonymous	0.465	41	45.0	0.912	0.00000309	651
Loss of Function	-0.773	6	4.27	1.40	3.42e-7	84

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: 0.667
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0777

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