GOLGA3

protein-coding

golgin A3, the group of Golgins

Gene summary

The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes a member of the golgin family of proteins which are localized to the Golgi. Its encoded protein has been postulated to play a role in nuclear transport and Golgi apparatus localization. Several alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Feb 2010]

MANE transcript

NM_001389683.1

Inheritance

ClinVar variants

U:259B:31

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr12:132,768,902-132,829,143

External References & Databases

Ensembl (ENSG00000090615)

Transcript & Mutation Effects

hg38 • Region Span ~60.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

primary ciliary dyskinesiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0016575

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GOLGA3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 264

not providedTotal: 14

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001389683.1. 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			2 clinvar	7 clinvar	2 clinvar	11
missense			250 clinvar	21 clinvar	1 clinvar	272
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	259	28	3	290

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001389683.1	RefSeq	NP_001376612.1	23	MANE Select
ENST00000450791.8	Ensembl	ENSP00000410378.2	23	MANE Select
NM_001172557.2	RefSeq	NP_001166028.1	15	Standard
NM_001389684.1	RefSeq	NP_001376613.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

intra-Golgi vesicle-mediated transport
spermatogenesis

Molecular Function

transporter activity
protein binding
cadherin binding

Cellular Component

Golgi membrane
nucleus
nucleoplasm
nucleolus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000204726
Coding exons: 23
Length: 59950
Individuals with no LoFs: 125656
Homozygous LoFs: 0
Heterozygous LoFs: 92
Defined: 125748
p: 0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0549	878	883	0.995	0.0000564	9733
Missense (PolyPhen)		288	318.79	0.90341		3731
Synonymous	-1.15	437	408	1.07	0.0000300	2907
Loss of Function	5.98	20	76.4	0.262	0.00000398	839

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0013	notable
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.0015	0.0015	notable
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0.00036	0.00036	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Golgi auto-antigen; probably involved in maintaining Golgi structure.;

Recessive Scores

pRec: 0.133

Intolerance Scores

LoFtool: 0.462
RVIS EVS: -0.57
RVIS percentile EVS: 18.97

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.829

Gene Damage Prediction

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