GOLGA6A

protein-coding

golgin A6 family member A, the group of Golgin related

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. The protein encoded by this gene is a member of the golgin family of proteins, whose members localize to the Golgi. This gene is found in a large, low copy repeat sequence or duplicon that is found in multiple copies, that are greather than 90% similar, on chromosome 15. Duplicons are associated with deletions, inversions and other chromosome rearrangements that underlie genomic disease. The protein encoded by this gene is thought to be a functional golgin protein while the majority of the related copies of this gene are thought to be transcribed pseudogenes. [provided by RefSeq, Jul 2008]

Previous symbols:

GOLGA6

MANE transcript

NM_001038640.2

Inheritance

—

ClinVar variants

U:82B:15

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr15:74,069,857-74,082,550

External References & Databases

Ensembl (ENSG00000159289)

Transcript & Mutation Effects

hg38 • Region Span ~12.7 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 GOLGA6A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 5

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001038640.2. 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				4 clinvar		4
missense			82 clinvar	11 clinvar		93
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	82	15	0	97

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001038640.2	RefSeq	NP_001033729.2	18	MANE Select
ENST00000290438.3	Ensembl	ENSP00000290438.3	18	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

Golgi organization
spindle assembly

Cellular Component

Golgi cis cisterna
Golgi apparatus
cis-Golgi network
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290438
Coding exons: 18
Length: 12694
Individuals with no LoFs: 125547
Homozygous LoFs: 0
Heterozygous LoFs: 131
Defined: 125678
p: 0.000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.294	108	99.7	1.08	0.00000588	4276
Missense (PolyPhen)		19	17.353	1.0949		1144
Synonymous	0.899	31	38.1	0.815	0.00000227	1163
Loss of Function	0.451	8	9.50	0.842	4.05e-7	484

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0024	0.0022	notable
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00032	0.00032	rare
South Asian	0.0017	0.0017	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0773

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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