GOLGA6A

Chr 15

golgin A6 family member A

Also known as: GLP, GOLGA6

NCBI Gene: 342096 ENSG00000159289 UniProt: Q9NYA3

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]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.50

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.50LOEUF

pLI 0.000

Z-score 0.45

OE 0.84 (0.49–1.50)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.29Z-score

OE missense 1.08 (0.93–1.27)

108 obs / 99.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.84 (0.49–1.50)

0≤0.351.4

Missense OE?1.08 (0.93–1.27)

0≤0.61.4

Synonymous OE?0.81

0≤1.21.6

LoF obs/exp: 8 / 9.5Missense obs/exp: 108 / 99.7Syn Z: 0.90

Background carrier burden — how many people carry a rare variant somewhere in GOLGA6A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 86

122 rare PASS variants

Rare truncating (LoF)

1 in 360

38 rare PASS variants

Rare synonymous (reference)

1 in 120

43 rare PASS variants

Rare missense and truncating variants are carried at similar rates in GOLGA6A; this gene does not show strong loss-of-function constraint by this measure. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 120	1 in 480
South Asian	~43k	1 in 110	1 in 260
Remaining (unassigned)	~30k	1 in 180	1 in 1,600
European (Finnish)	~27k	1 in 340	1 in 1,400
Admixed American	~22k	1 in 120	1 in 380
African / African American	~21k	1 in 150	1 in 950
East Asian	~20k	1 in 120	1 in 1,400
Ashkenazi Jewish	~13k	1 in 210	none seen
Middle Eastern	~2,864	≈ 1 in 720	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 5 of 18 coding exons well covered in gnomAD exomes; exons 1, 3, 4, 5, 6 and 7 more poorly covered; exon 17 marginal. Genomes: 2 of 18 (exons 1, 2, 3, 4, 5 and 11 more below).? see exons ↓