HTR1D

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

Basic information

Region (hg38): 1:23191894-23217502

Previous symbols: [ "HTRL" ]

Links

ENSG00000179546 ∙ NCBI:3352 ∙ OMIM:182133 ∙ HGNC:5289 ∙ Uniprot:P28221 ∙ 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 HTR1D gene.

• Inborn genetic diseases (23 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HTR1D 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	2
missense			23		1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	3

Variants in HTR1D

This is a list of pathogenic ClinVar variants found in the HTR1D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23193094-C-G		not specified	Uncertain significance (Jun 06, 2023)
1-23193129-C-T		not specified	Uncertain significance (Oct 13, 2023)
1-23193238-G-A		not specified	Uncertain significance (Oct 20, 2021)
1-23193268-A-C		not specified	Uncertain significance (Aug 16, 2022)
1-23193329-C-G		not specified	Uncertain significance (Mar 20, 2023)
1-23193333-T-G		not specified	Uncertain significance (Mar 07, 2024)
1-23193353-C-A		not specified	Uncertain significance (Mar 12, 2024)
1-23193363-A-G		not specified	Uncertain significance (Mar 24, 2023)
1-23193367-C-T		not specified	Uncertain significance (Sep 28, 2022)
1-23193387-T-G		not specified	Uncertain significance (Dec 19, 2023)
1-23193421-A-G		not specified	Uncertain significance (Oct 27, 2023)
1-23193426-G-A			Benign (May 22, 2018)
1-23193437-A-C		not specified	Uncertain significance (May 06, 2022)
1-23193456-G-A		not specified	Uncertain significance (Jan 31, 2022)
1-23193484-T-G		not specified	Uncertain significance (Nov 09, 2023)
1-23193498-G-A		not specified	Uncertain significance (Jun 11, 2021)
1-23193508-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-23193520-G-C		not specified	Uncertain significance (Nov 30, 2021)
1-23193541-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-23193555-C-T		not specified	Uncertain significance (May 26, 2023)
1-23193556-G-A		not specified	Uncertain significance (May 23, 2023)
1-23193598-T-C		not specified	Uncertain significance (May 18, 2022)
1-23193625-T-C		not specified	Uncertain significance (Mar 28, 2022)
1-23193662-C-T			Benign (May 21, 2018)
1-23193717-C-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HTR1D	protein_coding	protein_coding	ENST00000374619	1	4230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000641	0.750	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0899	221	225	0.983	0.0000134	2427
Missense in Polyphen		91	98.051	0.92809		1096
Synonymous	0.271	97	100	0.966	0.00000630	839
Loss of Function	0.957	6	9.12	0.658	4.57e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor for 5-hydroxytryptamine (serotonin). Also functions as a receptor for ergot alkaloid derivatives, various anxiolytic and antidepressant drugs and other 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. Regulates the release of 5-hydroxytryptamine in the brain, and thereby affects neural activity. May also play a role in regulating the release of other neurotransmitters. May play a role in vasoconstriction. {ECO:0000269|PubMed:10452531, ECO:0000269|PubMed:1565658, ECO:0000269|PubMed:1652050}.
• 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: 0.210

Intolerance Scores

• loftool: 0.216
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.513
• hipred: N
• hipred_score: 0.495
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.804

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Htr1d
• Phenotype: normal phenotype

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;intestine smooth muscle contraction;regulation of locomotion;vasoconstriction;regulation of behavior;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