PTH2R

parathyroid hormone 2 receptor, the group of Parathyroid hormone receptors

Basic information

Region (hg38): 2:208359714-208854503

Previous symbols: [ "PTHR2" ]

Links

ENSG00000144407 ∙ NCBI:5746 ∙ OMIM:601469 ∙ HGNC:9609 ∙ Uniprot:P49190 ∙ 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 PTH2R gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTH2R 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	3	5
missense			40	4		44
nonsense				2		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding						0
Total	0	0	40	8	3

Variants in PTH2R

This is a list of pathogenic ClinVar variants found in the PTH2R region.

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

Position	Type	Phenotype	Significance	ClinVar
2-208407049-C-A			Benign/Likely benign (Nov 01, 2022)
2-208407071-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-208407123-G-A		PTH2R-related disorder	Likely benign (Jun 01, 2023)
2-208407126-C-G		PTH2R-related disorder	Likely benign (May 28, 2019)
2-208428205-A-T		not specified	Uncertain significance (Sep 14, 2022)
2-208428217-C-A		not specified	Uncertain significance (Jun 29, 2023)
2-208428225-A-G		not specified	Uncertain significance (Feb 16, 2023)
2-208428291-C-G		not specified	Uncertain significance (Apr 07, 2022)
2-208437603-C-A		PTH2R-related disorder	Likely benign (Feb 09, 2021)
2-208437608-G-T		not specified	Uncertain significance (Jan 03, 2024)
2-208437621-C-T		not specified	Uncertain significance (Dec 21, 2022)
2-208437630-A-G		PTH2R-related disorder	Likely benign (Jun 07, 2022)
2-208437787-A-G		not specified	Uncertain significance (Feb 10, 2022)
2-208437788-T-A		PTH2R-related disorder	Uncertain significance (Oct 04, 2023)
2-208437820-A-C		PTH2R-related disorder	Uncertain significance (Dec 23, 2023)
2-208437828-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-208437843-T-A		not specified	Uncertain significance (Dec 19, 2023)
2-208437849-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-208437864-G-A		not specified	Uncertain significance (Mar 22, 2023)
2-208442385-T-C		not specified	Uncertain significance (Feb 15, 2023)
2-208442425-C-T		Syndromic intellectual disability	Likely pathogenic (Mar 26, 2017)
2-208442442-C-T		not specified	Uncertain significance (Jan 26, 2023)
2-208443359-G-A		not specified	Uncertain significance (Aug 01, 2022)
2-208443391-G-A		PTH2R-related disorder • not specified	Uncertain significance (Jan 04, 2022)
2-208443420-C-G		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTH2R	protein_coding	protein_coding	ENST00000272847	13	494790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-20	0.00138	122560	30	3158	125748	0.0128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.774	333	296	1.13	0.0000151	3604
Missense in Polyphen		128	112.77	1.135		1437
Synonymous	0.282	105	109	0.966	0.00000587	1038
Loss of Function	-0.133	30	29.2	1.03	0.00000151	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0131	0.0130
Ashkenazi Jewish	0.00873	0.00857
East Asian	0.000709	0.000707
Finnish	0.00584	0.00584
European (Non-Finnish)	0.0214	0.0213
Middle Eastern	0.000709	0.000707
South Asian	0.00367	0.00360
Other	0.0128	0.0126

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This is a specific receptor for parathyroid hormone. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase. PTH2R may be responsible for PTH effects in a number of physiological systems. It may play a significant role in pancreatic function. PTH2R presence in neurons indicates that it may function as a neurotransmitter receptor (By similarity). {ECO:0000250}.
• Pathway: Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Class B Secretin-like;Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Class B/2 (Secretin family receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.928
• rvis_EVS: -0.66
• rvis_percentile_EVS: 15.91

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.378
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.517

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pth2r

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cold-induced thermogenesis
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: parathyroid hormone receptor activity;protein binding;G protein-coupled peptide receptor activity;peptide hormone binding