HTR7

5-hydroxytryptamine receptor 7, the group of 5-hydroxytryptamine receptors, G protein-coupled

Basic information

Region (hg38): 10:90740823-90858039

Links

ENSG00000148680 ∙ NCBI:3363 ∙ OMIM:182137 ∙ HGNC:5302 ∙ Uniprot:P34969 ∙ 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 HTR7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR7 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			25	1	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	2

Variants in HTR7

This is a list of pathogenic ClinVar variants found in the HTR7 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-90742486-T-A		not specified	Uncertain significance (Mar 22, 2025)
10-90742528-T-C		not specified	Uncertain significance (Dec 16, 2022)
10-90743610-T-C		not specified	Uncertain significance (Nov 06, 2023)
10-90743617-G-A		not specified	Likely benign (Jun 16, 2024)
10-90743626-G-C		not specified	Uncertain significance (Mar 16, 2024)
10-90743643-G-C			Benign (Dec 31, 2019)
10-90748887-T-C		not specified	Uncertain significance (Jul 10, 2024)
10-90748889-C-A		not specified	Uncertain significance (Apr 11, 2025)
10-90748891-T-C		not specified	Uncertain significance (Dec 25, 2024)
10-90748969-G-A		not specified	Uncertain significance (Jun 24, 2022)
10-90748978-A-T		not specified	Uncertain significance (Oct 10, 2023)
10-90749131-C-A		not specified	Uncertain significance (Apr 11, 2025)
10-90749137-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-90749362-T-G		not specified	Uncertain significance (Mar 10, 2025)
10-90749418-T-C		not specified	Uncertain significance (May 20, 2025)
10-90749433-C-T		not specified	Uncertain significance (Apr 13, 2023)
10-90749491-A-T		not specified	Uncertain significance (Nov 14, 2024)
10-90749497-T-C		not specified	Uncertain significance (Nov 15, 2024)
10-90857169-G-A		not specified	Uncertain significance (Mar 27, 2025)
10-90857257-T-C		not specified	Uncertain significance (May 31, 2023)
10-90857261-G-T		not specified	Uncertain significance (Aug 16, 2021)
10-90857329-G-A		not specified	Uncertain significance (Jul 19, 2023)
10-90857409-A-C		not specified	Uncertain significance (May 30, 2024)
10-90857433-T-C		not specified	Uncertain significance (Apr 14, 2025)
10-90857436-A-C		not specified	Uncertain significance (Mar 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR7	protein_coding	protein_coding	ENST00000336152	4	117094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0454	0.950	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	197	278	0.708	0.0000141	3117
Missense in Polyphen		57	112.77	0.50546		1304
Synonymous	0.0954	120	121	0.989	0.00000651	986
Loss of Function	2.47	5	15.5	0.323	8.08e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000268	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
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);Ras signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;Excitatory Neural Signalling Through 5-HTR 7 and Serotonin ;GPCRs, Other;Ras Signaling;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: 0.153

Intolerance Scores

• loftool: 0.400
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.588
• hipred: Y
• hipred_score: 0.698
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.376

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr7
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: smooth muscle contraction;G protein-coupled receptor signaling pathway;G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger;chemical synaptic transmission;circadian rhythm;blood circulation;vasoconstriction;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;neurotransmitter receptor activity