PIGR

polymeric immunoglobulin receptor, the group of V-set domain containing

Basic information

Region (hg38): 1:206928521-206946466

Links

ENSG00000162896 ∙ NCBI:5284 ∙ OMIM:173880 ∙ HGNC:8968 ∙ Uniprot:P01833 ∙ 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 PIGR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PIGR 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			29	6	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	29	7	1

Variants in PIGR

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

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

Position	Type	Phenotype	Significance	ClinVar
1-206930356-C-T		not specified	Likely benign (Mar 20, 2023)
1-206931730-G-T		not specified	Uncertain significance (Oct 17, 2023)
1-206932486-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-206932507-C-A		not specified	Likely benign (Jun 18, 2024)
1-206933133-G-A		IgA glomerulonephritis	Uncertain significance (Jan 01, 2006)
1-206934449-T-G		not specified	Uncertain significance (Aug 12, 2022)
1-206934470-T-C		not specified	Uncertain significance (Mar 29, 2023)
1-206934471-A-G		not specified	Uncertain significance (Sep 06, 2022)
1-206934480-C-T		not specified	Uncertain significance (Apr 16, 2024)
1-206934525-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-206934564-C-T		not specified	Uncertain significance (Apr 18, 2023)
1-206935558-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-206935600-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-206935636-C-T		not specified	Uncertain significance (Mar 31, 2023)
1-206935683-C-T		not specified	Uncertain significance (Nov 18, 2022)
1-206935696-C-A		not specified	Uncertain significance (Apr 05, 2023)
1-206935725-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-206935726-T-C			Likely benign (Oct 01, 2022)
1-206935771-C-T			Benign (Nov 06, 2018)
1-206935785-T-G		not specified	Uncertain significance (Feb 21, 2024)
1-206935788-A-G		not specified	Uncertain significance (Jul 13, 2022)
1-206935806-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-206935822-G-A			Benign (Nov 06, 2018)
1-206937140-G-T		not specified	Uncertain significance (Mar 01, 2024)
1-206937308-T-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PIGR	protein_coding	protein_coding	ENST00000356495	10	17949

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.813	0.187	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	386	455	0.849	0.0000269	4955
Missense in Polyphen		87	148.16	0.5872		1769
Synonymous	-0.853	218	203	1.08	0.0000137	1574
Loss of Function	4.25	6	31.9	0.188	0.00000162	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000356	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000659	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This receptor binds polymeric IgA and IgM at the basolateral surface of epithelial cells. The complex is then transported across the cell to be secreted at the apical surface. During this process a cleavage occurs that separates the extracellular (known as the secretory component) from the transmembrane segment.
• Pathway: Intestinal immune network for IgA production - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System;IL4-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.197

Intolerance Scores

• loftool: 0.393
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.83

Haploinsufficiency Scores

• pHI: 0.0911
• hipred: N
• hipred_score: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.342

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pigr
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; digestive/alimentary phenotype; immune system phenotype

Gene ontology

• Biological process: detection of chemical stimulus involved in sensory perception of bitter taste;retina homeostasis;immunoglobulin transcytosis in epithelial cells mediated by polymeric immunoglobulin receptor;epidermal growth factor receptor signaling pathway;Fc receptor signaling pathway;receptor clustering;neutrophil degranulation
• Cellular component: extracellular space;plasma membrane;integral component of plasma membrane;azurophil granule membrane;receptor complex;extracellular exosome
• Molecular function: polymeric immunoglobulin receptor activity