PGRMC1

progesterone receptor membrane component 1, the group of Membrane associated progesterone receptor family

Basic information

Region (hg38): X:119236245-119244466

Links

ENSG00000101856 ∙ NCBI:10857 ∙ OMIM:300435 ∙ HGNC:16090 ∙ Uniprot:O00264 ∙ 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 PGRMC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGRMC1 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					1	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	1

Variants in PGRMC1

This is a list of pathogenic ClinVar variants found in the PGRMC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-119236480-C-G		not specified	Uncertain significance (Jul 10, 2024)
X-119236507-G-A			Benign (Sep 11, 2018)
X-119236533-G-C		not specified	Uncertain significance (Feb 24, 2025)
X-119236553-C-T		not specified	Uncertain significance (Nov 16, 2022)
X-119236571-C-T		not specified	Uncertain significance (May 29, 2024)
X-119236574-C-T		not specified	Uncertain significance (Apr 19, 2024)
X-119236587-C-G		not specified	Uncertain significance (May 22, 2023)
X-119236589-G-T		not specified	Uncertain significance (Mar 12, 2024)
X-119236590-C-T		not specified	Uncertain significance (Dec 10, 2024)
X-119236634-A-T		not specified	Uncertain significance (Aug 02, 2021)
X-119236635-T-C		Genetic non-acquired premature ovarian failure	Likely pathogenic (Oct 01, 2019)
X-119236688-C-T		not specified	Uncertain significance (Jul 02, 2024)
X-119240371-G-C		not specified	Uncertain significance (May 18, 2023)
X-119240372-A-T		not specified	Uncertain significance (Aug 30, 2021)
X-119240398-G-C		Genetic non-acquired premature ovarian failure	Likely pathogenic (Oct 01, 2019)
X-119240404-C-T		not specified	Uncertain significance (Jan 24, 2025)
X-119243160-A-G		PGRMC1-related disorder	Likely benign (Feb 20, 2023)
X-119243165-G-A		not specified	Uncertain significance (Feb 03, 2025)
X-119243199-C-T		Genetic non-acquired premature ovarian failure • PGRMC1-related disorder	Uncertain significance (Apr 05, 2023)
X-119243202-T-C		not specified	Uncertain significance (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGRMC1	protein_coding	protein_coding	ENST00000217971	3	8214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.671	0.309	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0800	78	80.0	0.975	0.00000553	1271
Missense in Polyphen		20	29.228	0.68427		473
Synonymous	1.15	28	36.8	0.760	0.00000268	402
Loss of Function	1.76	0	3.62	0.00	2.28e-7	68

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a progesterone-binding protein complex (PubMed:28396637). Binds progesterone (PubMed:25675345). Has many reported cellular functions (heme homeostasis, interaction with CYPs). {ECO:0000269|PubMed:25675345, ECO:0000303|PubMed:28396637}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.204
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.429
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgrmc1
• Phenotype: endocrine/exocrine gland phenotype; reproductive system 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;membrane;smooth endoplasmic reticulum membrane;specific granule membrane;neuron projection;neuronal cell body;cell body;synapse
• Molecular function: amyloid-beta binding;steroid binding;protein binding