ERGIC3

ERGIC and golgi 3

Basic information

Region (hg38): 20:35542038-35557634

Previous symbols: [ "SDBCAG84", "C20orf47" ]

Links

ENSG00000125991 ∙ NCBI:51614 ∙ OMIM:616971 ∙ HGNC:15927 ∙ Uniprot:Q9Y282 ∙ 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 ERGIC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERGIC3 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding			1			1
Total	0	0	14	0	1

Variants in ERGIC3

This is a list of pathogenic ClinVar variants found in the ERGIC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35542561-A-G		not specified	Uncertain significance (Dec 28, 2023)
20-35547414-C-G		not specified	Uncertain significance (May 04, 2023)
20-35547433-C-T		not specified	Uncertain significance (Dec 05, 2022)
20-35547447-G-C		not specified	Uncertain significance (Apr 15, 2024)
20-35547448-A-G		not specified	Uncertain significance (Mar 15, 2024)
20-35548534-C-T		not specified	Uncertain significance (Feb 27, 2024)
20-35548604-G-T		not specified	Uncertain significance (Mar 04, 2024)
20-35548618-A-G		not specified	Uncertain significance (Feb 28, 2023)
20-35548666-G-A		not specified	Uncertain significance (May 04, 2022)
20-35554380-G-A		not specified	Uncertain significance (May 05, 2023)
20-35555071-A-G		not specified	Uncertain significance (Nov 27, 2023)
20-35555076-G-A		See cases	Uncertain significance (Oct 13, 2020)
20-35556029-A-G			Benign (Jul 31, 2018)
20-35556221-C-T		Developmental disorder	Likely pathogenic (Sep 19, 2022)
20-35556269-G-C		not specified	Uncertain significance (Jul 15, 2021)
20-35556978-G-A			Benign (Jul 31, 2018)
20-35557024-G-T		not specified	Uncertain significance (Feb 02, 2024)
20-35557097-C-G		not specified	Uncertain significance (Nov 03, 2023)
20-35557199-T-G		not specified	Uncertain significance (Apr 04, 2024)
20-35557443-C-T		not specified	Uncertain significance (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERGIC3	protein_coding	protein_coding	ENST00000357394	14	15636

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000224	0.996	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	160	225	0.710	0.0000128	2562
Missense in Polyphen		41	69.583	0.58923		778
Synonymous	-0.936	103	91.6	1.12	0.00000559	717
Loss of Function	2.52	12	25.8	0.464	0.00000139	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000170	0.000158
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.898
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.300
• hipred: Y
• hipred_score: 0.639
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.304

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ergic3

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
• Cellular component: 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