GP2

protein-coding

glycoprotein 2

Gene summary

This gene encodes an integral membrane protein that is secreted from intracellular zymogen granules and associates with the plasma membrane via glycosylphosphatidylinositol (GPI) linkage. The encoded protein binds pathogens such as enterobacteria, thereby playing an important role in the innate immune response. The C-terminus of this protein is related to the C-terminus of the protein encoded by the neighboring gene, uromodulin (UMOD). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

MANE transcript

NM_001502.4

Inheritance

—

ClinVar variants

U:79B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr16:20,309,574-20,327,808

External References & Databases

Ensembl (ENSG00000169347)

Transcript & Mutation Effects

hg38 • Region Span ~18.2 kb

Loading mutation effect viewer...

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 GP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001502.4. 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	3 clinvar	4
missense			78 clinvar	7 clinvar	1 clinvar	86
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	8	4	91

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001502.4	RefSeq	NP_001493.2	10	MANE Select
ENST00000302555.10	Ensembl	ENSP00000304044.6	10	MANE Select
NM_001007240.3	RefSeq	NP_001007241.2	11	Standard
NM_001007241.3	RefSeq	NP_001007242.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Cellular Component

extracellular region
plasma membrane
anchored component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381362
Coding exons: 11
Length: 18237
Individuals with no LoFs: 125573
Homozygous LoFs: 1
Heterozygous LoFs: 173
Defined: 125747
p: 0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.696	274	308	0.888	0.0000164	3523
Missense (PolyPhen)		67	91.152	0.73504		1118
Synonymous	-1.23	137	120	1.14	0.00000647	1040
Loss of Function	-0.249	31	29.5	1.05	0.00000167	303

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.0012	0.0012	notable
European (Non-Finnish)	0.00075	0.00074	rare
South Asian	0.00036	0.00036	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.175

Intolerance Scores

LoFtool: 0.103
RVIS EVS: -0.4
RVIS percentile EVS: 26.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.159

Gene Damage Prediction

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