HCAR3

hydroxycarboxylic acid receptor 3, the group of Hydroxycarboxylic acid receptors

Basic information

Region (hg38): 12:122714756-122716811

Previous symbols: [ "GPR109B" ]

Links

ENSG00000255398 ∙ NCBI:8843 ∙ OMIM:606039 ∙ HGNC:16824 ∙ Uniprot:P49019 ∙ 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 HCAR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HCAR3 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				1		1
missense			19	2		21
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	3	0

Variants in HCAR3

This is a list of pathogenic ClinVar variants found in the HCAR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-122715648-T-C		not specified	Uncertain significance (Sep 11, 2024)
12-122715681-A-G		not specified	Uncertain significance (Feb 27, 2023)
12-122715717-C-T		not specified	Uncertain significance (Oct 20, 2021)
12-122715747-G-A		not specified	Uncertain significance (Oct 26, 2022)
12-122715753-C-T		not specified	Uncertain significance (Sep 16, 2021)
12-122715757-C-T			Likely benign (Sep 01, 2022)
12-122715782-C-T		not specified	Uncertain significance (Oct 25, 2024)
12-122715794-C-T		not specified	Likely benign (Jul 10, 2024)
12-122715930-G-A		not specified	Uncertain significance (Nov 12, 2021)
12-122715950-G-A		not specified	Uncertain significance (May 26, 2024)
12-122715963-G-A		not specified	Likely benign (Nov 17, 2022)
12-122715981-G-A		not specified	Uncertain significance (Nov 28, 2024)
12-122715986-C-T		not specified	Uncertain significance (Mar 14, 2023)
12-122716076-T-A		not specified	Uncertain significance (Oct 25, 2024)
12-122716091-C-T		not specified	Uncertain significance (Mar 28, 2023)
12-122716187-T-C		not specified	Uncertain significance (Dec 28, 2022)
12-122716195-G-C		not specified	Uncertain significance (Sep 25, 2023)
12-122716231-G-C		not specified	Uncertain significance (Oct 27, 2022)
12-122716272-C-G		not specified	Uncertain significance (May 11, 2022)
12-122716272-C-T		not specified	Likely benign (Dec 04, 2024)
12-122716355-C-T		not specified	Uncertain significance (Mar 02, 2023)
12-122716373-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-122716383-T-G		not specified	Uncertain significance (Jan 03, 2024)
12-122716431-C-T		not specified	Likely benign (Nov 08, 2022)
12-122716437-G-A		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HCAR3	protein_coding	protein_coding	ENST00000528880	1	2137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.86e-8	0.0460	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0107	228	228	0.998	0.0000142	2540
Missense in Polyphen		93	94.022	0.98913		1141
Synonymous	-0.874	104	93.3	1.12	0.00000565	769
Loss of Function	-1.27	9	5.73	1.57	3.34e-7	61

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: Receptor for 3-OH-octanoid acid mediates a negative feedback regulation of adipocyte lipolysis to counteract prolipolytic influences under conditions of physiological or pathological increases in beta-oxidation rates. Acts as a low affinity receptor for nicotinic acid. This pharmacological effect requires nicotinic acid doses that are much higher than those provided by a normal diet. {ECO:0000269|PubMed:12522134, ECO:0000269|PubMed:19561068}.
• Pathway: cAMP signaling pathway - Homo sapiens (human);GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Hydroxycarboxylic acid-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hcar2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;cell junction
• Molecular function: G protein-coupled receptor activity