HTR5A

5-hydroxytryptamine receptor 5A, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 7:155070323-155087392

Links

ENSG00000157219 ∙ NCBI:3361 ∙ OMIM:601305 ∙ HGNC:5300 ∙ Uniprot:P47898 ∙ 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 HTR5A gene.

• Inborn genetic diseases (12 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR5A 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					5	5
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	5

Variants in HTR5A

This is a list of pathogenic ClinVar variants found in the HTR5A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-155070967-G-C		not specified	Uncertain significance (Jan 09, 2024)
7-155070978-G-C		Malignant tumor of prostate	Uncertain significance (-)
7-155071009-C-T		not specified	Uncertain significance (Jul 30, 2023)
7-155071020-G-A		not specified	Uncertain significance (Mar 29, 2022)
7-155071080-G-T		not specified	Uncertain significance (Mar 01, 2023)
7-155071089-A-G		not specified	Uncertain significance (Jan 19, 2024)
7-155071104-C-G		not specified	Uncertain significance (Jun 22, 2021)
7-155071199-C-T			Benign (Dec 31, 2019)
7-155071297-C-T		not specified	Uncertain significance (Jun 01, 2023)
7-155071383-A-G		not specified	Uncertain significance (Jul 15, 2021)
7-155071466-C-T			Benign (Dec 31, 2019)
7-155071520-C-T			Benign (Mar 05, 2018)
7-155071565-G-C		not specified	Uncertain significance (Jan 19, 2024)
7-155071583-G-T		not specified	Uncertain significance (Aug 02, 2022)
7-155071629-G-A		not specified	Uncertain significance (Apr 17, 2023)
7-155084173-C-A		not specified	Uncertain significance (May 11, 2022)
7-155084202-C-T			Benign (Dec 31, 2019)
7-155084203-G-T		not specified	Uncertain significance (Dec 13, 2023)
7-155084234-C-A		not specified	Uncertain significance (Jan 24, 2023)
7-155084244-G-C		not specified	Uncertain significance (Jan 31, 2024)
7-155084262-C-T			Benign (Dec 31, 2019)
7-155084309-T-C		not specified	Uncertain significance (Jan 03, 2024)
7-155084338-C-T		not specified	Uncertain significance (Jan 16, 2024)
7-155084386-T-A		not specified	Uncertain significance (Sep 25, 2023)
7-155084416-C-T		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR5A	protein_coding	protein_coding	ENST00000287907	2	15426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00629	0.918	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.181	237	245	0.967	0.0000175	2299
Missense in Polyphen		72	81.128	0.88749		807
Synonymous	-0.229	116	113	1.03	0.00000884	764
Loss of Function	1.52	5	10.3	0.487	4.45e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000133	0.000114
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is one of the several different receptors for 5- hydroxytryptamine (serotonin), a biogenic hormone that functions as a neurotransmitter, a hormone, and a mitogen. The activity of this receptor is mediated by G proteins.
• Pathway: Serotonergic synapse - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Signaling by GPCR;Signal Transduction;Serotonin receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.524
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.521
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.193

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr5a
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting serotonin receptor signaling pathway;chemical synaptic transmission;cAMP-mediated signaling;hippocampus development;response to estradiol
• Cellular component: rough endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of plasma membrane;dendrite;perikaryon;integral component of postsynaptic specialization membrane
• Molecular function: G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity;serotonin binding