HTR1E

5-hydroxytryptamine receptor 1E, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 6:86937528-87016679

Links

ENSG00000168830 ∙ NCBI:3354 ∙ OMIM:182132 ∙ HGNC:5291 ∙ Uniprot:P28566 ∙ 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 HTR1E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR1E 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	2
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	1

Variants in HTR1E

This is a list of pathogenic ClinVar variants found in the HTR1E region.

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

Position	Type	Phenotype	Significance	ClinVar
6-87015389-A-G		not specified	Uncertain significance (Sep 17, 2021)
6-87015577-C-G		not specified	Likely benign (Sep 12, 2023)
6-87015670-C-T			Likely benign (Apr 10, 2018)
6-87015725-G-A		not specified	Uncertain significance (Dec 15, 2022)
6-87015738-C-T		not specified	Uncertain significance (Nov 03, 2023)
6-87015753-C-T		not specified	Uncertain significance (Apr 06, 2023)
6-87015824-C-T		not specified	Uncertain significance (Oct 14, 2023)
6-87015904-G-A			Benign (Mar 29, 2018)
6-87015945-G-A		not specified	Uncertain significance (Aug 20, 2023)
6-87016032-T-C		not specified	Uncertain significance (Dec 09, 2024)
6-87016058-T-C		not specified	Uncertain significance (Aug 02, 2023)
6-87016089-C-G		not specified	Uncertain significance (Mar 24, 2023)
6-87016110-T-C		not specified	Uncertain significance (Feb 12, 2024)
6-87016133-C-A		not specified	Uncertain significance (Jul 16, 2024)
6-87016133-C-G		not specified	Uncertain significance (Dec 13, 2022)
6-87016134-C-A			Likely benign (Feb 08, 2018)
6-87016170-A-G		not specified	Uncertain significance (Feb 16, 2023)
6-87016221-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-87016295-G-A		not specified	Uncertain significance (Aug 16, 2021)
6-87016331-G-A		not specified	Uncertain significance (Jan 23, 2023)
6-87016422-A-C		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR1E	protein_coding	protein_coding	ENST00000305344	1	79326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.293	0.688	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	145	216	0.672	0.0000126	2399
Missense in Polyphen		56	100.53	0.55704		1108
Synonymous	0.120	87	88.4	0.984	0.00000547	753
Loss of Function	1.98	2	8.09	0.247	3.43e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for various alkaloids and psychoactive substances. Ligand binding causes a conformation change that triggers signaling via guanine nucleotide-binding proteins (G proteins) and modulates the activity of down-stream effectors, such as adenylate cyclase. Signaling inhibits adenylate cyclase activity. {ECO:0000269|PubMed:14744596, ECO:0000269|PubMed:1513320, ECO:0000269|PubMed:1608964, ECO:0000269|PubMed:1733778, ECO:0000269|PubMed:21422162}.
• Pathway: Serotonergic synapse - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Taste transduction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;GPCRs, Class A Rhodopsin-like;Monoamine GPCRs;Serotonin HTR1 Group and FOS Pathway;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: 0.119

Intolerance Scores

• loftool: 0.580
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.248
• hipred: Y
• hipred_score: 0.501
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.940

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;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;chemical synaptic transmission;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;dendrite
• Molecular function: G protein-coupled receptor activity;G protein-coupled serotonin receptor activity;protein binding;neurotransmitter receptor activity;serotonin binding