ERGIC3

protein-coding

ERGIC and golgi 3

Gene summary

Involved in endoplasmic reticulum to Golgi vesicle-mediated transport and positive regulation of intracellular protein transport. Located in membrane. Biomarker of lung adenocarcinoma. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

SDBCAG84
C20orf47

MANE transcript

NM_015966.3

Inheritance

ClinVar variants

P:1U:54B:2

Top phenotype

Developmental disorder

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr20:35,542,038-35,557,634

External References & Databases

Ensembl (ENSG00000125991)

Transcript & Mutation Effects

hg38 • Region Span ~15.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ERGIC3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 3

Developmental disorderTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015966.3. 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 clinvar	2
missense			46 clinvar			46
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	1	54	1	1	57

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 63 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015966.3	RefSeq	NP_057050.1	13	MANE Select
ENST00000348547.7	Ensembl	ENSP00000341358.2	13	MANE Select
NM_198398.2	RefSeq	NP_938408.1	14	Standard
ENST00000357394.8	Ensembl	ENSP00000349970.4	14	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

Cellular Component

endoplasmic reticulum
membrane
COPII-coated ER to Golgi transport vesicle
integral component of Golgi membrane
integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357394
Coding exons: 14
Length: 15636
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	160	225	0.710	0.0000128	2562
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00032	0.00032	rare
European (Non-Finnish)	0.00017	0.00016	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.304

Gene Damage Prediction

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