ERGIC2

ERGIC and golgi 2

Basic information

Region (hg38): 12:29337352-29381189

Links

ENSG00000087502 ∙ NCBI:51290 ∙ OMIM:612236 ∙ HGNC:30208 ∙ Uniprot:Q96RQ1 ∙ 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 ERGIC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERGIC2 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						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in ERGIC2

This is a list of pathogenic ClinVar variants found in the ERGIC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-29341166-T-C		not specified	Uncertain significance (Nov 04, 2022)
12-29341182-G-A		not specified	Uncertain significance (Apr 23, 2024)
12-29341211-A-G		not specified	Uncertain significance (Feb 13, 2025)
12-29341738-T-C		not specified	Uncertain significance (Feb 07, 2023)
12-29341745-G-A		not specified	Uncertain significance (Mar 02, 2023)
12-29341768-C-T		not specified	Uncertain significance (Jan 19, 2025)
12-29343140-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-29343170-T-C		not specified	Uncertain significance (Jan 03, 2024)
12-29343260-G-T		not specified	Uncertain significance (Dec 28, 2023)
12-29345454-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
12-29345484-T-C		not specified	Uncertain significance (Aug 14, 2023)
12-29349091-T-C		not specified	Uncertain significance (Sep 13, 2023)
12-29349118-T-C		not specified	Uncertain significance (Sep 01, 2024)
12-29349121-T-A		not specified	Uncertain significance (Apr 09, 2024)
12-29349135-T-G		not specified	Uncertain significance (Oct 27, 2021)
12-29350061-G-C		not specified	Uncertain significance (Nov 10, 2024)
12-29356418-T-C		not specified	Uncertain significance (Dec 09, 2024)
12-29356470-C-T		not specified	Uncertain significance (Nov 10, 2022)
12-29357644-G-A		not specified	Uncertain significance (Sep 26, 2022)
12-29357645-T-C		not specified	Likely benign (Jul 14, 2021)
12-29366888-C-G		not specified	Uncertain significance (Oct 26, 2022)
12-29366947-T-A		not specified	Uncertain significance (Dec 01, 2022)
12-29368259-C-A		not specified	Uncertain significance (Mar 14, 2025)
12-29368265-T-C		not specified	Uncertain significance (Aug 10, 2021)
12-29370115-T-C		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERGIC2	protein_coding	protein_coding	ENST00000360150	13	43838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0135	0.985	124774	0	17	124791	0.0000681

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	152	194	0.785	0.00000927	2482
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000125
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000905	0.0000883
Middle Eastern	0.000113	0.000111
South Asian	0.00	0.00
Other	0.000168	0.000165

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.841
• hipred: Y
• hipred_score: 0.517
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.284

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ergic2

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
• Cellular component: nucleus;nucleolus;cytoplasm;endoplasmic reticulum;membrane;COPII-coated ER to Golgi transport vesicle;integral component of Golgi membrane;integral component of endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding