HTR6

5-hydroxytryptamine receptor 6, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 1:19664874-19680966

Links

ENSG00000158748 ∙ NCBI:3362 ∙ OMIM:601109 ∙ HGNC:5301 ∙ Uniprot:P50406 ∙ 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 HTR6 gene.

• Inborn genetic diseases (21 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR6 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	5	7
missense			19	3	1	23
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	5	6

Variants in HTR6

This is a list of pathogenic ClinVar variants found in the HTR6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-19665776-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-19665805-G-C			Benign (Jun 26, 2018)
1-19665881-C-T		not specified	Uncertain significance (Apr 28, 2022)
1-19666017-G-A			Benign (Jun 18, 2018)
1-19666018-T-C		not specified	Uncertain significance (Feb 13, 2023)
1-19666019-A-G		not specified	Uncertain significance (Jul 27, 2022)
1-19666087-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-19666106-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-19666190-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-19666215-C-T			Benign (Jul 11, 2018)
1-19666234-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-19666259-T-C		not specified	Uncertain significance (Jul 27, 2021)
1-19666296-C-T			Benign (Jan 09, 2018)
1-19666358-G-T		not specified	Uncertain significance (Oct 03, 2022)
1-19666363-A-G		not specified	Uncertain significance (May 11, 2022)
1-19666411-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-19678583-G-A		not specified	Uncertain significance (Mar 07, 2023)
1-19678616-T-C		not specified	Uncertain significance (Dec 02, 2022)
1-19678635-G-C		not specified	Uncertain significance (Jan 26, 2023)
1-19678672-C-T			Likely benign (Jul 06, 2018)
1-19678922-G-A		not specified	Uncertain significance (Feb 22, 2024)
1-19678989-T-G		not specified	Uncertain significance (Dec 05, 2022)
1-19679018-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-19679060-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-19679105-C-T		not specified	Uncertain significance (May 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR6	protein_coding	protein_coding	ENST00000289753	3	14276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000185	0.724	125735	0	11	125746	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.343	276	293	0.944	0.0000186	2738
Missense in Polyphen		85	95.636	0.88879		1006
Synonymous	-0.915	154	140	1.10	0.00000892	1037
Loss of Function	0.953	7	10.3	0.680	4.42e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000169	0.000163
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.0000446	0.0000440
Middle Eastern	0.000169	0.000163
South Asian	0.00	0.00
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. It has a high affinity for tricyclic psychotropic drugs (By similarity). Controls pyramidal neurons migration during corticogenesis, through the regulation of CDK5 activity (By similarity). Is an activator of TOR signaling (PubMed:23027611). {ECO:0000250|UniProtKB:P31388, ECO:0000250|UniProtKB:Q9R1C8, ECO:0000269|PubMed:23027611}.
• 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 6 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: 0.151

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.435
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.334

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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

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;cerebral cortex cell migration;positive regulation of TOR signaling;G protein-coupled serotonin receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;cilium;dendrite
• Molecular function: G protein-coupled receptor activity;histamine receptor activity;G protein-coupled serotonin receptor activity;protein binding;neurotransmitter receptor activity