ERGIC1

endoplasmic reticulum-golgi intermediate compartment 1

Basic information

Region (hg38): 5:172834250-172952792

Links

ENSG00000113719 ∙ NCBI:57222 ∙ OMIM:617946 ∙ HGNC:29205 ∙ Uniprot:Q969X5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• arthrogryposis multiplex congenita 2, neurogenic type (Supportive), mode of inheritance: AR
• arthrogryposis multiplex congenita 2, neurogenic type (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Arthrogryposis multiplex congenita 2, neurogenic type	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	5491443; 28317099

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ERGIC1 gene.

• Inborn genetic diseases (9 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERGIC1 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			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	9	2	1

Variants in ERGIC1

This is a list of pathogenic ClinVar variants found in the ERGIC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-172909752-C-T		not specified	Uncertain significance (May 23, 2023)
5-172909753-A-T		not specified	Uncertain significance (Nov 21, 2023)
5-172914744-G-A		not specified	Uncertain significance (Mar 29, 2023)
5-172914756-T-A		Arthrogryposis multiplex congenita 2, neurogenic type	Pathogenic (Jul 31, 2020)
5-172914767-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-172914768-A-C		not specified	Uncertain significance (Sep 16, 2021)
5-172914966-C-T			Benign (Feb 01, 2024)
5-172915596-C-T			Likely benign (Mar 01, 2023)
5-172924023-G-A		not specified	Uncertain significance (Oct 26, 2021)
5-172926541-C-T		ERGIC1-related disorder	Likely benign (Sep 17, 2019)
5-172935183-C-T		ERGIC1-related disorder	Likely benign (Nov 17, 2022)
5-172935197-G-A		ERGIC1-related disorder	Likely benign (May 01, 2023)
5-172935218-A-C		not specified	Uncertain significance (Oct 26, 2022)
5-172935230-A-G		not specified	Uncertain significance (May 24, 2023)
5-172935272-A-G		not specified	Uncertain significance (Oct 25, 2023)
5-172935281-C-T		not specified	Uncertain significance (Aug 10, 2021)
5-172935309-C-T		not specified	Uncertain significance (Feb 06, 2023)
5-172950700-C-T		ERGIC1-related disorder	Likely benign (Jun 07, 2019)
5-172950722-T-C		not specified	Uncertain significance (Nov 06, 2023)
5-172950725-G-A		Flexion contracture	Likely pathogenic (-)
5-172950742-G-A		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERGIC1	protein_coding	protein_coding	ENST00000393784	10	118411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.647	0.352	125724	0	24	125748	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	128	183	0.698	0.0000115	1933
Missense in Polyphen		44	77.096	0.57072		789
Synonymous	1.03	70	81.9	0.855	0.00000638	540
Loss of Function	3.07	3	16.4	0.183	8.01e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000650	0.000647
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible role in transport between endoplasmic reticulum and Golgi. {ECO:0000303|PubMed:15308636}.
• Disease: DISEASE: Arthrogryposis multiplex congenita, neurogenic type (AMCN) [MIM:208100]: A form of arthrogryposis multiplex congenita, a heterogeneous group of disorders characterized by multiple joint contractures resulting, in some cases, from reduced or absent fetal movements. AMCN is due to a neurogenic defect and is characterized by congenital immobility of the limbs with fixation of multiple joints, and muscle wasting. AMCN transmission pattern is consistent with autosomal recessive inheritance in several families. Penetrance may be incomplete in females. {ECO:0000269|PubMed:28317099}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.350
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.290
• hipred: Y
• hipred_score: 0.749
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ergic1

Gene ontology

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