GOLGA6D

Chr 15

golgin A6 family member D

NCBI Gene: 653643 ENSG00000140478 UniProt: P0CG33

Predicted to be involved in Golgi organization. Predicted to be located in Golgi apparatus. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.93

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.93LOEUF

pLI 0.000

Z-score -1.18

OE 1.53 (0.87–1.93)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.80Z-score

OE missense 1.25 (1.06–1.47)

102 obs / 81.8 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?1.53 (0.87–1.93)

0≤0.351.4

Missense OE?1.25 (1.06–1.47)

0≤0.61.4

Synonymous OE?1.54

0≤1.21.6

LoF obs/exp: 9 / 5.9Missense obs/exp: 102 / 81.8Syn Z: -2.52

Background carrier burden — how many people carry a rare variant somewhere in GOLGA6D?

gnomAD v4 · ~729k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 110

116 rare PASS variants

Rare truncating (LoF)

1 in 580

35 rare PASS variants

Rare synonymous (reference)

1 in 150

56 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GOLGA6D. 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)	~555k	1 in 280	1 in 680
South Asian	~43k	1 in 210	1 in 970
Remaining (unassigned)	~30k	1 in 160	1 in 510
European (Finnish)	~27k	1 in 2,300	none seen
Admixed American	~22k	1 in 170	1 in 510
East Asian	~20k	1 in 110	1 in 500
African / African American	~19k	1 in 130	1 in 890
Ashkenazi Jewish	~13k	1 in 2,500	≈ 1 in 3,100
Middle Eastern	~2,777	1 in 300	1 in 280

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): 4 of 18 coding exons well covered in gnomAD exomes; exons 1, 2, 3, 4, 5 and 7 more poorly covered; exons 8, 16 marginal. Genomes: 0 of 18 (exons 1, 2, 3, 4, 5 and 13 more below).? see exons ↓