ERGIC3

ERGIC and golgi 3

Basic information

Region (hg38): 20:35542038-35557634

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

Links

ENSG00000125991NCBI:51614OMIM:616971HGNC:15927Uniprot:Q9Y282AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
12
clinvar
12
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
1
non coding
1
clinvar
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)3090165
20-35547414-C-G not specified Uncertain significance (May 04, 2023)2514689
20-35547433-C-T not specified Uncertain significance (Dec 05, 2022)2227892
20-35547447-G-C not specified Uncertain significance (Apr 15, 2024)3276335
20-35547448-A-G not specified Uncertain significance (Mar 15, 2024)3276333
20-35548534-C-T not specified Uncertain significance (Feb 27, 2024)3090166
20-35548604-G-T not specified Uncertain significance (Mar 04, 2024)3090167
20-35548618-A-G not specified Uncertain significance (Feb 28, 2023)2490941
20-35548666-G-A not specified Uncertain significance (May 04, 2022)2287168
20-35554380-G-A not specified Uncertain significance (May 05, 2023)2516743
20-35555071-A-G not specified Uncertain significance (Nov 27, 2023)3090170
20-35555076-G-A See cases Uncertain significance (Oct 13, 2020)983448
20-35556029-A-G Benign (Jul 31, 2018)777543
20-35556221-C-T Developmental disorder Likely pathogenic (Sep 19, 2022)2661907
20-35556269-G-C not specified Uncertain significance (Jul 15, 2021)2374577
20-35556978-G-A Benign (Jul 31, 2018)777544
20-35557024-G-T not specified Uncertain significance (Feb 02, 2024)3090171
20-35557097-C-G not specified Uncertain significance (Nov 03, 2023)3090163
20-35557199-T-G not specified Uncertain significance (Apr 04, 2024)3276334
20-35557443-C-T not specified Uncertain significance (Nov 03, 2023)3090164

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ERGIC3protein_codingprotein_codingENST00000357394 1415636
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002240.9961257170311257480.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.551602250.7100.00001282562
Missense in Polyphen4169.5830.58923778
Synonymous-0.93610391.61.120.00000559717
Loss of Function2.521225.80.4640.00000139281

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001480.000148
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.0003230.000323
European (Non-Finnish)0.0001700.000158
Middle Eastern0.000.00
South Asian0.00006530.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ergic3
Phenotype

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
Molecular function