PGR

progesterone receptor, the group of Nuclear receptor subfamily 3 group C

Basic information

Region (hg38): 11:101029623-101129813

Links

ENSG00000082175 ∙ NCBI:5241 ∙ OMIM:607311 ∙ HGNC:8910 ∙ Uniprot:P06401 ∙ 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 PGR gene.

• Inborn genetic diseases (28 variants)
• not provided (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGR 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				5	9	14
missense			28	1	5	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	28	6	14

Variants in PGR

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

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

Position	Type	Phenotype	Significance	ClinVar
11-101039138-G-T		not specified	Uncertain significance (Sep 26, 2022)
11-101041987-C-T			Benign (Jul 05, 2018)
11-101051458-T-C		not specified	Uncertain significance (May 18, 2022)
11-101062676-G-A			Benign (May 24, 2018)
11-101062708-G-C			Benign (Aug 07, 2018)
11-101091797-G-T			Benign (Aug 04, 2018)
11-101125999-G-A			Benign (Aug 16, 2018)
11-101126013-T-C		not specified	Uncertain significance (Aug 30, 2021)
11-101126118-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-101127443-T-C		not specified	Uncertain significance (Feb 05, 2024)
11-101127456-G-A		not specified	Uncertain significance (Aug 12, 2021)
11-101127464-T-G			Benign (Nov 20, 2018)
11-101127496-G-A			Likely benign (Apr 11, 2018)
11-101127596-C-A		not specified	Uncertain significance (Feb 22, 2023)
11-101127599-G-C		not specified	Uncertain significance (May 04, 2022)
11-101127627-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-101127633-A-C		not specified	Uncertain significance (Aug 12, 2021)
11-101127728-A-G		not specified	Uncertain significance (Nov 22, 2021)
11-101127748-G-C			Likely benign (Jun 26, 2018)
11-101127766-C-G			Likely benign (Jun 08, 2018)
11-101127770-G-C		not specified	Uncertain significance (Nov 30, 2021)
11-101127800-G-C		not specified	Uncertain significance (Dec 21, 2022)
11-101127827-G-C		not specified	Uncertain significance (May 31, 2023)
11-101127840-G-C		not specified	Uncertain significance (Jul 06, 2021)
11-101127887-T-G		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGR	protein_coding	protein_coding	ENST00000325455	8	100901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0510	0.949	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	426	507	0.840	0.0000242	5880
Missense in Polyphen		121	202.08	0.59878		2475
Synonymous	-0.435	224	216	1.04	0.0000106	1983
Loss of Function	3.91	9	33.4	0.269	0.00000165	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000881	0.0000881
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.0000963	0.0000924
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.000171	0.000163
South Asian	0.0000670	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Depending on the isoform, progesterone receptor functions as transcriptional activator or repressor. {ECO:0000269|PubMed:10757795, ECO:0000269|PubMed:1587864, ECO:0000269|PubMed:9407067, ECO:0000305}.; FUNCTION: Isoform B: Transcriptional activator of several progesteron-dependent promoters in a variety of cell types. Involved in activation of SRC-dependent MAPK signaling on hormone stimulation. {ECO:0000269|PubMed:7969170}.
• Pathway: Oocyte meiosis - Homo sapiens (human);Breast cancer - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);NHR;Nuclear Receptors;Signaling by ERBB4;Ovarian Infertility Genes;Signal Transduction;Gene expression (Transcription);how progesterone initiates the oocyte maturation;Generic Transcription Pathway;HSP90 chaperone cycle for steroid hormone receptors (SHR);Cellular responses to stress;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription;Cellular responses to external stimuli;Signaling by Nuclear Receptors;Estrogen-dependent gene expression;Nuclear signaling by ERBB4;Signaling by ERBB4;Signaling by Receptor Tyrosine Kinases;ESR-mediated signaling;Validated nuclear estrogen receptor alpha network;Cellular roles of Anthrax toxin (Consensus)

Recessive Scores

• pRec: 0.530

Haploinsufficiency Scores

• pHI: 0.139
• hipred: Y
• hipred_score: 0.834
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.499

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgr
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; embryo phenotype

Zebrafish Information Network

• Gene name: pgr
• Affected structure: oocyte stage V
• Phenotype tag: abnormal
• Phenotype quality: non-functional

Gene ontology

• Biological process: ovulation from ovarian follicle;epithelial cell maturation;transcription initiation from RNA polymerase II promoter;signal transduction;cell-cell signaling;negative regulation of gene expression;paracrine signaling;positive regulation of transcription by RNA polymerase II;lung alveolus development;regulation of epithelial cell proliferation;progesterone receptor signaling pathway;tertiary branching involved in mammary gland duct morphogenesis
• Cellular component: nucleoplasm;mitochondrial outer membrane;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;steroid hormone receptor activity;nuclear receptor activity;steroid binding;protein binding;zinc ion binding;enzyme binding;identical protein binding;ATPase binding