PTH1R
protein-codingparathyroid hormone 1 receptor, the group of Parathyroid hormone receptors
Gene summary
The protein encoded by this gene is a member of the G-protein coupled receptor family 2. This protein is a receptor for parathyroid hormone (PTH) and for parathyroid hormone-like hormone (PTHLH). The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system. Defects in this receptor are known to be the cause of Jansen's metaphyseal chondrodysplasia (JMC), chondrodysplasia Blomstrand type (BOCD), as well as enchodromatosis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, May 2010]
- PTHR
- PTHR1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008970
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0007982
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0008970
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007434
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0008970
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010803
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007982
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007982
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007434
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0010803
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007434
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0007434
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008970
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010803
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0010803
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008970
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0007982
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PTH1R variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000316.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 81 | 89 | |||
| missense | 9 | 6 | 232 | 14 | 1 | 262 |
| nonsense | 4 | 2 | 1 | 7 | ||
| start loss | 0 | |||||
| frameshift | 3 | 1 | 1 | 5 | ||
| splice donor/acceptor (+/-2bp) | 3 | 3 | 4 | 10 | ||
| Total | 19 | 12 | 246 | 95 | 1 | 373 |
Highest pathogenic variant AF is 0.000005712472
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000307.1 | 14 | MANE Select | |
| Ensembl | ENSP00000402723.1 | 14 | MANE Select | |
| RefSeq | NP_001171673.1 | 14 | Standard | |
| Ensembl | ENSP00000321999.4 | 14 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| pth1ra | Danio rerio | Structure: hypochord Quality: decreased process quality abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human)
- Neuroactive ligand-receptor interaction - Homo sapiens (human)
- Osteoblast Signaling
- GPCRs, Class B Secretin-like
- Endochondral Ossification
Biological Process
- skeletal system development
- chondrocyte differentiation
- osteoblast development
- cellular calcium ion homeostasis
- cell surface receptor signaling pathway
Molecular Function
- parathyroid hormone receptor activity
- protein binding
- G protein-coupled peptide receptor activity
- peptide hormone binding
- protein homodimerization activity
Cellular Component
- nucleus
- cytoplasm
- plasma membrane
- integral component of plasma membrane
- basolateral plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000313049
- Coding exons
- 14
- Length
- 26052
- Individuals with no LoFs
- 125740
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125748
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 272 | 360 | 0.755 | 0.0000232 | 3801 |
| Missense (PolyPhen) | 104 | 152.63 | 0.68137 | 1682 | ||
| Synonymous | 0.0638 | 152 | 153 | 0.993 | 0.0000103 | 1201 |
| Loss of Function | 3.94 | 6 | 28.8 | 0.208 | 0.00000144 | 326 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor for parathyroid hormone and for parathyroid hormone-related peptide. The activity of this receptor is mediated by G proteins which activate adenylyl cyclase and also a phosphatidylinositol-calcium second messenger system. {ECO:0000269|PubMed:20172855, ECO:0000269|PubMed:27160269, ECO:0000269|PubMed:8397094}.;
- Disease
- DISEASE: Jansen metaphyseal chondrodysplasia (JMC) [MIM:156400]: Rare autosomal dominant disorder characterized by a short-limbed dwarfism associated with hypercalcemia and normal or low serum concentrations of the two parathyroid hormones. {ECO:0000269|PubMed:10487664, ECO:0000269|PubMed:15240651, ECO:0000269|PubMed:27160269, ECO:0000269|PubMed:7701349, ECO:0000269|PubMed:8703170, ECO:0000269|PubMed:9178745}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Chondrodysplasia Blomstrand type (BOCD) [MIM:215045]: Severe skeletal dysplasia. {ECO:0000269|PubMed:9745456}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Enchondromatosis multiple (ENCHOM) [MIM:166000]: A condition characterized by multiple formation of enchondromas, benign neoplasms derived from mesodermal cells that form cartilage. Enchondromas remain within the substance of a cartilage or bone. Clinical problems caused by enchondromas include skeletal deformity and the potential for malignant change to osteosarcoma. {ECO:0000269|PubMed:11850620}. Note=The disease may be caused by mutations affecting the gene represented in this entry.; DISEASE: Eiken skeletal dysplasia (EISD) [MIM:600002]: A rare skeletal dysplasia characterized by severely retarded ossification, principally of the epiphyses, pelvis, hands and feet, as well as by abnormal modeling of the bones in hands and feet, abnormal persistence of cartilage in the pelvis and mild growth retardation. {ECO:0000269|PubMed:15525660}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Primary failure of tooth eruption (PFE) [MIM:125350]: Rare condition that has high penetrance and variable expressivity and in which tooth retention occurs without evidence of any obvious mechanical interference. Instead, malfunction of the eruptive mechanism itself appears to cause nonankylosed permanent teeth to fail to erupt, although the eruption pathway has been cleared by bone resorption. {ECO:0000269|PubMed:19061984}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- LoFtool
- 0.528
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 58.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.305
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |