PTH2

parathyroid hormone 2, the group of Receptor ligands

Basic information

Region (hg38): 19:49422419-49423441

Links

ENSG00000142538 ∙ NCBI:113091 ∙ OMIM:608386 ∙ HGNC:30828 ∙ Uniprot:Q96A98 ∙ 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 PTH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTH2 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						0
missense			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in PTH2

This is a list of pathogenic ClinVar variants found in the PTH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49422475-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-49422475-G-T		not specified	Uncertain significance (Oct 26, 2021)
19-49422500-T-G		not specified	Uncertain significance (Oct 12, 2022)
19-49422544-C-A		not specified	Uncertain significance (Nov 30, 2022)
19-49422544-C-G		not specified	Uncertain significance (Jul 19, 2023)
19-49422545-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-49422560-A-G		not specified	Uncertain significance (May 06, 2024)
19-49422571-T-C		not specified	Uncertain significance (Feb 14, 2023)
19-49422596-G-T		not specified	Uncertain significance (Nov 12, 2024)
19-49422622-G-A		not specified	Uncertain significance (Feb 01, 2025)
19-49422625-C-T		not specified	Uncertain significance (Feb 03, 2022)
19-49422632-G-C		not specified	Uncertain significance (Mar 29, 2023)
19-49423222-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-49423227-G-C		not specified	Uncertain significance (Jan 03, 2022)
19-49423236-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-49423264-A-T		not specified	Uncertain significance (Oct 29, 2024)
19-49423267-G-C		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTH2	protein_coding	protein_coding	ENST00000270631	2	1028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00262	0.355	124780	0	27	124807	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.440	61	52.1	1.17	0.00000237	576
Missense in Polyphen		18	15.803	1.139		162
Synonymous	1.37	20	29.4	0.680	0.00000134	253
Loss of Function	-0.963	3	1.66	1.81	7.16e-8	21

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000256	0.000222
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000192	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a potent and selective agonist of PTH2R resulting in adenyl cyclase activation and intracellular calcium levels elevation. Induces protein kinase C beta activation, recruitment of beta-arrestin and PTH2R internalization. May inhibit cell proliferation via its action on PTH2R activation. Neuropeptide which may also have a role in spermatogenesis. May activate nociceptors and nociceptive circuits. {ECO:0000269|PubMed:11861531, ECO:0000269|PubMed:12559132, ECO:0000269|PubMed:12754053, ECO:0000269|PubMed:14988434}.
• Pathway: 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: 0.135

Intolerance Scores

• loftool: 0.343
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.63

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.290

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pth2
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;neuropeptide signaling pathway
• Cellular component: extracellular region