PTGFRN

protein-coding

prostaglandin F2 receptor inhibitor, the group of V-set domain containing|CD molecules

Gene summary

Predicted to be involved in myoblast fusion involved in skeletal muscle regeneration. Predicted to act upstream of or within lipid droplet organization. Located in cell surface. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020440.4

Inheritance

—

ClinVar variants

U:140B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr1:116,909,916-116,990,353

External References & Databases

Ensembl (ENSG00000134247)

Transcript & Mutation Effects

hg38 • Region Span ~80.4 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 PTGFRN variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 136

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020440.4. 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			5 clinvar	4 clinvar	4 clinvar	13
missense			133 clinvar	6 clinvar		139
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	140	10	4	154

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020440.4	RefSeq	NP_065173.2	9	MANE Select
ENST00000393203.3	Ensembl	ENSP00000376899.2	9	MANE Select
ENST00000881332.1	Ensembl	ENSP00000551391.1	8	Standard
ENST00000881332.2	Ensembl	ENSP00000551391.1	8	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ptgfrn	Danio rerio	Structure: mRNA destabilization Quality: decreased occurrence abnormal

Gene / Model

Organism

Observed Phenotype

ptgfrn

Danio rerio

Structure: mRNA destabilization

Quality: decreased occurrence

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Prostaglandin Synthesis and Regulation

Biological Process

lipid droplet organization

Molecular Function

protein binding

Cellular Component

endoplasmic reticulum membrane
Golgi apparatus
cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393203
Coding exons: 9
Length: 80302
Individuals with no LoFs: 125698
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125748
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	440	551	0.799	0.0000362	5668
Missense (PolyPhen)		157	236.9	0.66272		2532
Synonymous	0.862	221	238	0.929	0.0000165	1819
Loss of Function	3.80	13	38.4	0.338	0.00000220	386

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00023	0.00017	rare
Ashkenazi Jewish	0.00091	0.00050	rare
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.00059	0.00059	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits the binding of prostaglandin F2-alpha (PGF2- alpha) to its specific FP receptor, by decreasing the receptor number rather than the affinity constant. Functional coupling with the prostaglandin F2-alpha receptor seems to occur (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.160

Intolerance Scores

LoFtool: 0.568
RVIS EVS: -0.24
RVIS percentile EVS: 36.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.629

Gene Damage Prediction

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