PGRMC2

progesterone receptor membrane component 2, the group of Membrane associated progesterone receptor family

Basic information

Region (hg38): 4:128269237-128288829

Links

ENSG00000164040 ∙ NCBI:10424 ∙ OMIM:607735 ∙ HGNC:16089 ∙ Uniprot:O15173 ∙ 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 PGRMC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGRMC2 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in PGRMC2

This is a list of pathogenic ClinVar variants found in the PGRMC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-128271338-T-C		not specified	Uncertain significance (Jan 20, 2023)
4-128272385-C-T		not specified	Uncertain significance (Jan 17, 2023)
4-128272517-G-A		not specified	Uncertain significance (Dec 03, 2021)
4-128287376-G-C		not specified	Uncertain significance (Aug 17, 2022)
4-128287397-T-C		not specified	Uncertain significance (Jul 27, 2024)
4-128287420-T-C		not specified	Uncertain significance (Oct 26, 2023)
4-128287465-C-A		not specified	Uncertain significance (Jun 11, 2021)
4-128287482-G-T		not specified	Uncertain significance (May 30, 2024)
4-128287497-C-A		not specified	Uncertain significance (Jan 07, 2025)
4-128287502-G-A		not specified	Uncertain significance (Jun 10, 2024)
4-128287510-G-C		not specified	Uncertain significance (Apr 09, 2024)
4-128287520-G-A		not specified	Uncertain significance (Sep 27, 2024)
4-128287544-C-G		not specified	Uncertain significance (Aug 04, 2023)
4-128287549-C-T		not specified	Uncertain significance (Apr 27, 2022)
4-128287559-G-A		not specified	Uncertain significance (Feb 15, 2023)
4-128287562-G-A		not specified	Uncertain significance (Feb 28, 2024)
4-128287574-C-T		not specified	Uncertain significance (Dec 31, 2024)
4-128287606-G-A		not specified	Uncertain significance (Nov 12, 2021)
4-128287612-A-G		not specified	Uncertain significance (Aug 21, 2023)
4-128287640-C-T		not specified	Uncertain significance (Mar 01, 2023)
4-128287643-C-A		not specified	Uncertain significance (Jun 06, 2023)
4-128287678-C-T		Hirschsprung disease, susceptibility to, 1	Uncertain significance (Nov 18, 2016)
4-128287710-A-C		not specified	Uncertain significance (Mar 14, 2025)
4-128287726-T-C		not specified	Uncertain significance (Dec 16, 2024)
4-128287790-T-G		not specified	Uncertain significance (Aug 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGRMC2	protein_coding	protein_coding	ENST00000520121	3	19588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.680	0.316	125446	0	2	125448	0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.842	106	133	0.795	0.00000614	1541
Missense in Polyphen		19	36.36	0.52255		505
Synonymous	-1.70	73	56.7	1.29	0.00000272	529
Loss of Function	2.30	1	8.01	0.125	3.98e-7	100

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000642	0.0000620
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000916	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for steroids. {ECO:0000305}.

Recessive Scores

• pRec: 0.160

Haploinsufficiency Scores

• pHI: 0.245
• hipred: N
• hipred_score: 0.450
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000998

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgrmc2
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism 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); reproductive system phenotype; hematopoietic system phenotype; embryo phenotype; immune system phenotype

Gene ontology

• Biological process: steroid hormone mediated signaling pathway
• Cellular component: nuclear envelope;membrane;integral component of membrane
• Molecular function: steroid hormone receptor activity;steroid binding;protein binding