HTR4

5-hydroxytryptamine receptor 4, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 5:148446041-148677235

Links

ENSG00000164270 ∙ NCBI:3360 ∙ OMIM:602164 ∙ HGNC:5299 ∙ Uniprot:Q13639 ∙ 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 HTR4 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)
• Lung adenocarcinoma (2 variants)
• Squamous cell carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR4 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			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1	2	5
Total	0	0	12	2	4

Variants in HTR4

This is a list of pathogenic ClinVar variants found in the HTR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-148483241-T-G		not specified	Uncertain significance (Jul 20, 2021)
5-148483255-C-T			Benign (Aug 04, 2018)
5-148483280-A-G		not specified	Uncertain significance (Jan 03, 2024)
5-148483286-C-T		not specified	Uncertain significance (May 03, 2023)
5-148484289-T-C			Benign (Mar 30, 2018)
5-148484353-A-G		not specified	Uncertain significance (Aug 17, 2021)
5-148509245-G-T		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
5-148509464-A-G			Benign (Jun 12, 2018)
5-148509465-T-C		not specified	Uncertain significance (Oct 02, 2023)
5-148509570-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-148509587-C-G		not specified	Uncertain significance (Dec 19, 2023)
5-148509783-C-T		not specified	Uncertain significance (Apr 05, 2023)
5-148509792-C-T		not specified	Uncertain significance (Jan 30, 2024)
5-148509823-C-T		not specified	Uncertain significance (Jan 18, 2022)
5-148509888-A-T		not specified	Uncertain significance (Aug 13, 2021)
5-148509891-C-T		not specified	Uncertain significance (Mar 31, 2023)
5-148509939-A-G		not specified	Uncertain significance (Jan 03, 2024)
5-148509954-G-A		not specified	Uncertain significance (Oct 12, 2022)
5-148510001-C-G		not specified	Uncertain significance (Aug 30, 2022)
5-148510014-C-T		not specified	Uncertain significance (Dec 11, 2023)
5-148523291-G-T		not specified	Uncertain significance (Sep 29, 2023)
5-148548816-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-148550194-A-G		not specified	Uncertain significance (Nov 18, 2023)
5-148550246-C-T			Likely benign (Jun 06, 2018)
5-148629768-C-T		Lung adenocarcinoma	Likely benign (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR4	protein_coding	protein_coding	ENST00000360693	7	226204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0247	0.973	125733	0	14	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.696	218	249	0.876	0.0000136	2792
Missense in Polyphen		71	99.128	0.71624		1116
Synonymous	-0.229	102	99.1	1.03	0.00000599	853
Loss of Function	2.65	6	18.2	0.330	8.57e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.0000791
Middle Eastern	0.000171	0.000163
South Asian	0.0000327	0.0000327
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 that stimulate adenylate cyclase.
• Pathway: Serotonergic synapse - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;Excitatory Neural Signalling Through 5-HTR 4 and Serotonin;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Serotonin Receptor 4-6-7 and NR3C Signaling;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Serotonin receptors;Amine ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.726
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.0902
• hipred: Y
• hipred_score: 0.729
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr4
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs 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;chemical synaptic transmission;regulation of appetite;G protein-coupled serotonin receptor signaling pathway
• Cellular component: cytoplasm;endosome;plasma membrane;integral component of plasma membrane;membrane;dendrite
• Molecular function: G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;neurotransmitter receptor activity