PTGFRN

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

Basic information

Region (hg38): 1:116909915-116990353

Links

ENSG00000134247 ∙ NCBI:5738 ∙ OMIM:601204 ∙ HGNC:9601 ∙ Uniprot:Q9P2B2 ∙ 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 PTGFRN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTGFRN 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				2	4	6
missense			62	3		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	62	5	4

Variants in PTGFRN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-116910241-T-C		not specified	Uncertain significance (Dec 11, 2023)
1-116941729-C-T		not specified	Uncertain significance (May 14, 2024)
1-116941769-T-C		not specified	Uncertain significance (Feb 28, 2023)
1-116941808-A-T		not specified	Uncertain significance (Feb 26, 2024)
1-116941908-G-T		not specified	Uncertain significance (Aug 11, 2022)
1-116941959-C-T			Benign (Jun 11, 2018)
1-116941990-G-T		not specified	Uncertain significance (Dec 04, 2023)
1-116942062-G-C		not specified	Uncertain significance (Nov 09, 2021)
1-116942077-G-T		not specified	Uncertain significance (Dec 21, 2023)
1-116944712-C-T		not specified	Uncertain significance (Mar 28, 2024)
1-116944721-C-G		not specified	Uncertain significance (May 17, 2023)
1-116944722-G-A			Benign (Oct 19, 2017)
1-116944756-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-116944774-G-A		not specified	Uncertain significance (Sep 27, 2022)
1-116944834-G-C		not specified	Uncertain significance (Oct 18, 2021)
1-116944867-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-116944906-C-G		not specified	Uncertain significance (Feb 14, 2023)
1-116944910-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-116944915-G-T		not specified	Uncertain significance (Jul 16, 2021)
1-116944945-G-A			Likely benign (Jun 11, 2018)
1-116944961-T-C		not specified	Uncertain significance (Oct 26, 2022)
1-116944985-A-G			Likely benign (Apr 02, 2018)
1-116944991-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-116945020-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-116945057-C-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTGFRN	protein_coding	protein_coding	ENST00000393203	9	80302

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000476	1.00	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	440	551	0.799	0.0000362	5668
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000356	0.000355
Ashkenazi Jewish	0.000914	0.000496
East Asian	0.00	0.00
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000144	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000589	0.000588
Other	0.000173	0.000163

dbNSFP

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}.
• Pathway: Prostaglandin Synthesis and Regulation (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.568
• rvis_EVS: -0.24
• rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

• pHI: 0.293
• hipred: Y
• hipred_score: 0.622
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.629

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptgfrn
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ptgfrn
• Affected structure: mRNA destabilization
• Phenotype tag: abnormal
• Phenotype quality: decreased occurrence

Gene ontology

• Biological process: lipid droplet organization
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;cell surface;integral component of membrane
• Molecular function: protein binding