PIGR

protein-coding

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

Gene summary

This gene is a member of the immunoglobulin superfamily. The encoded poly-Ig receptor binds polymeric immunoglobulin molecules at the basolateral surface of epithelial cells; the complex is then transported across the cell to be secreted at the apical surface. A significant association was found between immunoglobulin A nephropathy and several SNPs in this gene.[provided by RefSeq, Sep 2009]

MANE transcript

NM_002644.4

Inheritance

—

ClinVar variants

U:92B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.19

Max pathogenic AF

—

Genomic locus

chr1:206,928,522-206,946,466

External References & Databases

Ensembl (ENSG00000162896)

Transcript & Mutation Effects

hg38 • Region Span ~17.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PIGR variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 94

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002644.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			86 clinvar	12 clinvar		98
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	92	14	0	106

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002644.4	RefSeq	NP_002635.2	10	MANE Select
ENST00000356495.5	Ensembl	ENSP00000348888.4	10	MANE Select
ENST00000860525.1	Ensembl	ENSP00000530584.1	10	Standard
ENST00000860526.1	Ensembl	ENSP00000530585.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Intestinal immune network for IgA production - Homo sapiens (human)
Neutrophil degranulation
Innate Immune System
Immune System
IL4-mediated signaling events

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

Molecular Function

polymeric immunoglobulin receptor activity

Cellular Component

extracellular space
plasma membrane
integral component of plasma membrane
azurophil granule membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000356495
Coding exons: 10
Length: 17949
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125748
p: 0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	386	455	0.849	0.0000269	4955
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.197

Intolerance Scores

LoFtool: 0.393
RVIS EVS: -0.42
RVIS percentile EVS: 25.83

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.342

Gene Damage Prediction

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