PGRMC2

protein-coding

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

Gene summary

Enables heme binding activity. Involved in adipose tissue development. Located in endoplasmic reticulum and nuclear envelope. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006320.6

Inheritance

—

ClinVar variants

U:37

Top phenotype

Hirschsprung disease, susceptibility to, 1

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr4:128,269,237-128,288,829

External References & Databases

Ensembl (ENSG00000164040)

Transcript & Mutation Effects

hg38 • Region Span ~19.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PGRMC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 1

Hirschsprung disease, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006320.6. 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.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			34 clinvar			34
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	37	0	0	37

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006320.6	RefSeq	NP_006311.3	3	MANE Select
ENST00000296425.10	Ensembl	ENSP00000296425.4	3	MANE Select
ENST00000394276.3	Ensembl	ENSP00000475242.1	2	Standard
ENST00000394276.4	Ensembl	ENSP00000475242.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

steroid hormone mediated signaling pathway

Molecular Function

steroid hormone receptor activity
steroid binding
protein binding

Cellular Component

nuclear envelope
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000520121
Coding exons: 3
Length: 19588
Individuals with no LoFs: 125446
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125448
p: 0.00000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.842	106	133	0.795	0.00000614	1541
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000064	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000092	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.160

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.000998

Gene Damage Prediction

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