PLRG1

pleiotropic regulator 1, the group of WD repeat domain containing|NTC associated proteins|NineTeen complex|Spliceosomal C complex

Basic information

Region (hg38): 4:154535005-154550400

Links

ENSG00000171566 ∙ NCBI:5356 ∙ OMIM:605961 ∙ HGNC:9089 ∙ Uniprot:O43660 ∙ 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 PLRG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLRG1 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					1	1
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	1

Variants in PLRG1

This is a list of pathogenic ClinVar variants found in the PLRG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-154537357-G-C		not specified	Uncertain significance (Aug 28, 2023)
4-154537417-C-T		not specified	Uncertain significance (Mar 17, 2023)
4-154537434-T-C		not specified	Uncertain significance (Oct 26, 2022)
4-154538029-C-T		not specified	Uncertain significance (Jul 27, 2022)
4-154538031-G-C		not specified	Uncertain significance (May 09, 2022)
4-154540038-T-C		not specified	Uncertain significance (Apr 01, 2024)
4-154540595-C-T		not specified	Uncertain significance (Dec 16, 2023)
4-154540637-G-T		not specified	Uncertain significance (Nov 29, 2023)
4-154540842-A-G			Benign (Jan 08, 2019)
4-154544449-T-C		not specified	Uncertain significance (Sep 21, 2023)
4-154544486-T-C		not specified	Uncertain significance (Jun 05, 2023)
4-154544489-T-C		not specified	Uncertain significance (Jan 26, 2023)
4-154545846-G-A		not specified	Uncertain significance (Jul 30, 2023)
4-154545861-C-T		not specified	Uncertain significance (Jan 22, 2024)
4-154545865-C-T		not specified	Uncertain significance (Oct 20, 2023)
4-154545871-C-G		not specified	Uncertain significance (May 03, 2023)
4-154545915-G-C		not specified	Uncertain significance (Aug 08, 2023)
4-154546148-C-T		not specified	Uncertain significance (Jul 21, 2021)
4-154546163-C-G		not specified	Uncertain significance (Dec 21, 2022)
4-154546199-C-T		not specified	Uncertain significance (Oct 05, 2023)
4-154546211-C-G		not specified	Uncertain significance (Dec 14, 2023)
4-154547023-G-A		not specified	Uncertain significance (Jun 03, 2022)
4-154547734-T-A		not specified	Uncertain significance (May 22, 2023)
4-154547750-T-A		not specified	Likely benign (Feb 17, 2023)
4-154547773-T-G		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLRG1	protein_coding	protein_coding	ENST00000499023	15	15430

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000895	125690	0	4	125694	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	167	283	0.590	0.0000144	3357
Missense in Polyphen		48	135.06	0.35539		1603
Synonymous	1.73	76	97.8	0.777	0.00000522	968
Loss of Function	4.89	3	33.5	0.0894	0.00000186	371

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:28502770, PubMed:28076346). Component of the PRP19-CDC5L complex that forms an integral part of the spliceosome and is required for activating pre-mRNA splicing (PubMed:11101529, PubMed:11544257). {ECO:0000269|PubMed:11101529, ECO:0000269|PubMed:11544257, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.555
• hipred: Y
• hipred_score: 0.825
• ghis: 0.646

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.497

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plrg1
• Phenotype: cellular phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: plrg1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• Biological process: mRNA splicing, via spliceosome;protein localization to nucleus;positive regulation of G1/S transition of mitotic cell cycle
• Cellular component: Prp19 complex;fibrillar center;nucleus;nucleoplasm;DNA replication factor A complex;nuclear speck;nuclear membrane;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;Cul4-RING E3 ubiquitin ligase complex
• Molecular function: protein binding