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.

not_specified (91 variants)
PTH2R-related_disorder (11 variants)
not_provided (8 variants)
Syndromic_intellectual_disability (1 variants)

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. These statistics are base on transcript: NM_000005048.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense		1 clinvar	91 clinvar	5 clinvar		97
nonsense				2 clinvar		2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	91	10	2

Loading clinvar variants...

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
Phenotype

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