PTH1R

protein-coding

parathyroid 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]

Previous symbols:
  • PTHR
  • PTHR1

MANE transcript

NM_000316.3

Inheritance

AR, AD

ClinVar variants

P:31U:246B:96

Top phenotype

Eiken syndrome; Chondrodysplasia, Blomstrand type; Metaphyseal chondrodysplasia, Jansen type; Failure of tooth eruption, primary

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr3:46,877,721-46,903,799

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

chondrodysplasia Blomstrand typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008970

Submitter: Genomics England PanelApp

metaphyseal chondrodysplasia, Jansen typeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007982

Submitter: G2P

chondrodysplasia Blomstrand typeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008970

Submitter: G2P

primary failure of tooth eruptionSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007434

Submitter: Orphanet

chondrodysplasia Blomstrand typeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008970

Submitter: Orphanet

Eiken syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010803

Submitter: Orphanet

metaphyseal chondrodysplasia, Jansen typeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007982

Submitter: Orphanet

metaphyseal chondrodysplasia, Jansen typeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007982

Submitter: PanelApp Australia

primary failure of tooth eruptionDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007434

Submitter: G2P

Eiken syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010803

Submitter: Labcorp Genetics (formerly Invitae)

primary failure of tooth eruptionSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007434

Submitter: Labcorp Genetics (formerly Invitae)

primary failure of tooth eruptionSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007434

Submitter: PanelApp Australia

chondrodysplasia Blomstrand typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008970

Submitter: Labcorp Genetics (formerly Invitae)

Eiken syndromeLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0010803

Submitter: Ambry Genetics

Eiken syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010803

Submitter: PanelApp Australia

chondrodysplasia Blomstrand typeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008970

Submitter: PanelApp Australia

metaphyseal chondrodysplasia, Jansen typeSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007982

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Eiken syndrome; Chondrodysplasia, Blomstrand type; Metaphyseal chondrodysplasia, Jansen type; Failure of tooth eruption, primaryAD/AR

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

Refs: 3975110; 6734674; 8276022; 7701349; 9268097; 9178745; 9649554; 9745456; 10664159; 12357475; 15525660; 17164305; 19061984; 20135246; 29987841Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTH1R variants in ClinVar

14 Conditions Cataloged
not providedTotal: 328
Metaphyseal chondrodysplasia, Jansen typeTotal: 127
Chondrodysplasia Blomstrand typeTotal: 122
Primary failure of tooth eruptionTotal: 105
Eiken syndromeTotal: 95
Inborn genetic diseasesTotal: 77
not specifiedTotal: 30
PTH1R-related disorderTotal: 20

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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
81
clinvar
89
missense
9
clinvar
6
clinvar
232
clinvar
14
clinvar
1
clinvar
262
nonsense
4
clinvar
2
clinvar
1
clinvar
7
start loss
0
frameshift
3
clinvar
1
clinvar
1
clinvar
5
splice donor/acceptor (+/-2bp)
3
clinvar
3
clinvar
4
clinvar
10
Total1912246951373

Highest pathogenic variant AF is 0.000005712472

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000316.3RefSeqNP_000307.114MANE Select
ENST00000449590.6EnsemblENSP00000402723.114MANE Select
NM_001184744.1RefSeqNP_001171673.114Standard
ENST00000313049.10EnsemblENSP00000321999.414Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
pth1raDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.652723600.7550.00002323801
Missense (PolyPhen)104152.630.681371682
Synonymous0.06381521530.9930.00001031201
Loss of Function3.94628.80.2080.00000144326

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000270.000026rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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