PAG1

phosphoprotein membrane anchor with glycosphingolipid microdomains 1

Basic information

Region (hg38): 8:80967810-81112068

Links

ENSG00000076641 ∙ NCBI:55824 ∙ OMIM:605767 ∙ HGNC:30043 ∙ Uniprot:Q9NWQ8 ∙ 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 PAG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAG1 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			17	3	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	17	4	1

Variants in PAG1

This is a list of pathogenic ClinVar variants found in the PAG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-80976560-T-C		not specified	Uncertain significance (Nov 21, 2022)
8-80976633-T-A			Likely benign (Nov 29, 2017)
8-80976678-C-T		not specified	Uncertain significance (Mar 24, 2023)
8-80976839-G-C		not specified	Uncertain significance (Nov 14, 2024)
8-80976845-G-A		not specified	Uncertain significance (Aug 05, 2023)
8-80980467-G-A		not specified	Uncertain significance (Aug 12, 2024)
8-80984929-A-C		not specified	Uncertain significance (Dec 06, 2024)
8-80984939-T-A		not specified	Uncertain significance (Jul 22, 2024)
8-80984942-C-T		not specified	Uncertain significance (Jun 17, 2024)
8-80984943-G-A		not specified	Uncertain significance (Dec 15, 2022)
8-80985017-T-C		not specified	Uncertain significance (Oct 22, 2024)
8-80985032-G-C		not specified	Uncertain significance (Oct 06, 2021)
8-80985053-T-C		not specified	Uncertain significance (Dec 09, 2024)
8-80985095-T-A		not specified	Uncertain significance (Sep 26, 2024)
8-80985200-A-G			Benign (Dec 31, 2019)
8-80985219-T-C		not specified	Uncertain significance (Nov 10, 2024)
8-80987418-C-A		not specified	Uncertain significance (Dec 13, 2022)
8-80987442-G-T		not specified	Uncertain significance (Dec 10, 2024)
8-80991491-G-T		not specified	Uncertain significance (Dec 06, 2024)
8-80993094-G-A			Likely benign (Apr 25, 2018)
8-80993161-C-T		not specified	Likely benign (Dec 08, 2023)
8-80993200-T-C		not specified	Likely benign (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAG1	protein_coding	protein_coding	ENST00000220597	6	144259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.978	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.992	206	250	0.824	0.0000137	2841
Missense in Polyphen		64	89.131	0.71804		1059
Synonymous	-0.0155	104	104	1.00	0.00000678	837
Loss of Function	2.52	6	17.3	0.347	8.15e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000186	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates TCR (T-cell antigen receptor)- mediated signaling in T-cells and FCER1 (high affinity immunoglobulin epsilon receptor)-mediated signaling in mast cells. Promotes CSK activation and recruitment to lipid rafts, which results in LCK inhibition. Inhibits immunological synapse formation by preventing dynamic arrangement of lipid raft proteins. May be involved in cell adhesion signaling. {ECO:0000269|PubMed:10790433}.
• Pathway: Signal Transduction;Phosphorylation of CD3 and TCR zeta chains;TCR signaling;TCR;Immune System;Adaptive Immune System;Signaling by EGFR;SHP2 signaling;CXCR4-mediated signaling events;GAB1 signalosome;BCR signaling pathway;Signaling by Receptor Tyrosine Kinases;TCR signaling in naïve CD8+ T cells;PDGFR-beta signaling pathway;TCR signaling in naïve CD4+ T cells (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.174
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.76

Haploinsufficiency Scores

• pHI: 0.313
• hipred: Y
• hipred_score: 0.553
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.425

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pag1
• Phenotype: immune system phenotype; hematopoietic system phenotype; normal phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: adaptive immune response;signal transduction;positive regulation of signal transduction;intracellular signal transduction;T cell receptor signaling pathway;regulation of T cell activation;negative regulation of T cell activation
• Cellular component: plasma membrane;integral component of membrane;membrane raft
• Molecular function: SH3/SH2 adaptor activity;protein binding;SH2 domain binding