COPZ1

protein-coding

COPI coat complex subunit zeta 1, the group of MicroRNA protein coding host genes|COPI coat complex

Gene summary

This gene encodes a subunit of the cytoplasmic coatamer protein complex, which is involved in autophagy and intracellular protein trafficking. The coatomer protein complex is comprised of seven subunits and functions as the coat protein of coat protein complex (COP)I-vesicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

Previous symbols:

COPZ

MANE transcript

NM_016057.3

Inheritance

—

ClinVar variants

P:1U:26B:2

Top phenotype

Neutropenia, severe congenital, 12, autosomal recessive

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr12:54,301,202-54,351,846

External References & Databases

Ensembl (ENSG00000111481)

Transcript & Mutation Effects

hg38 • Region Span ~50.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COPZ1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 3

Neutropenia, severe congenital, 12, autosomal recessiveTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016057.3. 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			21 clinvar			21
nonsense			1 clinvar			1
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	1	26	1	1	29

Highest pathogenic variant AF is 0.0000012392618

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016057.3	RefSeq	NP_057141.1	9	MANE Select
ENST00000262061.7	Ensembl	ENSP00000262061.2	9	MANE Select
NM_001271734.2	RefSeq	NP_001258663.1	8	Standard
NM_001271735.2	RefSeq	NP_001258664.1	8	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
copz1	Danio rerio	Structure: head Quality: decreased width abnormal

Gene / Model

Organism

Observed Phenotype

copz1

Danio rerio

Structure: head

Quality: decreased width

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Post-translational protein modification
Metabolism of proteins
Transport to the Golgi and subsequent modification

Biological Process

intracellular protein transport
endoplasmic reticulum to Golgi vesicle-mediated transport
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
intra-Golgi vesicle-mediated transport
toxin transport

Cellular Component

Golgi membrane
endoplasmic reticulum membrane
cytosol
COPI vesicle coat
transport vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262061
Coding exons: 9
Length: 50648
Individuals with no LoFs: 125694
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125696
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.766	75	96.1	0.780	0.00000493	1153
Missense (PolyPhen)		19	28.042	0.67756		377
Synonymous	0.137	36	37.1	0.971	0.00000195	324
Loss of Function	3.19	1	13.8	0.0726	7.33e-7	155

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.124

Intolerance Scores

LoFtool: 0.204
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.909

Gene Damage Prediction

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