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.

not_specified (43 variants)
not_provided (3 variants)

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. These statistics are base on transcript: NM_000018440.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			39 clinvar	5 clinvar	1 clinvar	45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	5	1

Loading clinvar variants...

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