PLGRKT

plasminogen receptor with a C-terminal lysine

Basic information

Region (hg38): 9:5357970-5437925

Previous symbols: [ "C9orf46" ]

Links

ENSG00000107020 ∙ NCBI:55848 ∙ OMIM:618444 ∙ HGNC:23633 ∙ Uniprot:Q9HBL7 ∙ 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 PLGRKT gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLGRKT 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in PLGRKT

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

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

Position	Type	Phenotype	Significance	ClinVar
9-5358285-A-G		not specified	Uncertain significance (Dec 28, 2023)
9-5361099-T-C		not specified	Uncertain significance (Mar 01, 2023)
9-5361161-A-G		not specified	Uncertain significance (Jun 08, 2022)
9-5361185-G-A		not specified	Uncertain significance (Aug 31, 2022)
9-5361186-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-5361772-G-C		not specified	Uncertain significance (Feb 17, 2022)
9-5361819-G-C		not specified	Uncertain significance (Aug 16, 2021)
9-5361866-T-A		not specified	Uncertain significance (Aug 30, 2022)
9-5431901-A-G		not specified	Uncertain significance (Jul 06, 2021)
9-5431910-T-C		not specified	Likely benign (Aug 16, 2022)
9-5431918-C-T		not specified	Uncertain significance (Apr 17, 2023)
9-5431941-T-C		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLGRKT	protein_coding	protein_coding	ENST00000223864	4	79906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.60e-8	0.0642	125707	0	35	125742	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	104	77.0	1.35	0.00000374	980
Missense in Polyphen		31	24.738	1.2531		301
Synonymous	-1.89	37	25.0	1.48	0.00000130	242
Loss of Function	-0.724	10	7.82	1.28	3.92e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000377	0.000305
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.000267	0.000261
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for plasminogen. Regulates urokinase plasminogen activator-dependent and stimulates tissue-type plasminogen activator-dependent cell surface plasminogen activation. Proposed to be part of a local catecholaminergic cell plasminogen activation system that regulates neuroendocrine prohormone processing. Involved in regulation of inflammatory response; regulates monocyte chemotactic migration and matrix metallproteinase activation, such as of MMP2 and MMP9. {ECO:0000269|PubMed:21940822}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.282
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plgrkt

Gene ontology

• Biological process: chemotaxis;inflammatory response;positive regulation of plasminogen activation
• Cellular component: integral component of plasma membrane
• Molecular function: protein binding