ERGIC2

protein-coding

ERGIC and golgi 2

Gene summary

ERGIC2, or PTX1, is a ubiquitously expressed nuclear protein that is downregulated in prostate carcinoma (Kwok et al., 2001 [PubMed 11445006]).[supplied by OMIM, Aug 2008]

MANE transcript

NM_016570.3

Inheritance

—

ClinVar variants

U:47B:2

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr12:29,337,352-29,381,189

External References & Databases

Ensembl (ENSG00000087502)

Transcript & Mutation Effects

hg38 • Region Span ~43.8 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 ERGIC2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 42

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Craniolenticulosutural dysplasiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016570.3. 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			1
missense			42 clinvar	2 clinvar		44
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	47	2	0	49

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016570.3	RefSeq	NP_057654.2	13	MANE Select
ENST00000360150.9	Ensembl	ENSP00000353270.4	13	MANE Select
ENST00000546509.5	Ensembl	ENSP00000447212.1	3	Standard
ENST00000546839.5	Ensembl	ENSP00000450042.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum

Molecular Function

protein binding

Cellular Component

nucleus
nucleolus
cytoplasm
endoplasmic reticulum
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000360150
Coding exons: 13
Length: 43838
Individuals with no LoFs: 124774
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 124791
p: 0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	152	194	0.785	0.00000927	2482
Missense (PolyPhen)		30	53.544	0.56029		688
Synonymous	0.689	54	60.8	0.888	0.00000285	678
Loss of Function	2.82	7	20.9	0.334	9.67e-7	281

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000065	rare
Latino/Admixed American	0.000060	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible role in transport between endoplasmic reticulum and Golgi. {ECO:0000250}.;

Recessive Scores

pRec: 0.0850

Intolerance Scores

LoFtool: 0.421
RVIS EVS: -0.34
RVIS percentile EVS: 30.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.284

Gene Damage Prediction

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