GOLGA2

Chr 9AR

golgin A2

Also known as: DEDHMB, GM130

NCBI Gene: 2801 ENSG00000167110 UniProt: Q08379 OMIM: 602580

This gene encodes a peripheral membrane protein that maintains Golgi apparatus structure, facilitates vesicle tethering and fusion, and plays essential roles in spindle pole assembly and centrosome organization during cell division. Mutations cause autosomal recessive developmental delays, intellectual disability, and skeletal abnormalities with onset in early childhood. The gene is highly constrained against loss-of-function variants (pLI 0.99, LOEUF 0.30), indicating that complete loss of protein function is likely incompatible with normal development.

OMIM ResearchSummary from RefSeq, UniProt

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 one of the golgins, a family of proteins localized to the Golgi. This encoded protein has been postulated to play roles in the stacking of Golgi cisternae and in vesicular transport. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of these variants has not been determined. [provided by RefSeq, Feb 2010]

OMIM ResearchGenerating clinical summary…

ARLOEUF 0.291 OMIM phenotype

Clinical Summary— GOLGA2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

11 unique Pathogenic / Likely Pathogenic· 151 VUS of 223 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.29LOEUF

pLI 0.988

Z-score 5.98

OE 0.18 (0.11–0.29)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

0.90Z-score

OE missense 0.89 (0.83–0.96)

520 obs / 581.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.18 (0.11–0.29)

0≤0.351.4

Missense OE?0.89 (0.83–0.96)

0≤0.61.4

Synonymous OE?0.92

0≤1.21.6

LoF obs/exp: 11 / 61.7Missense obs/exp: 520 / 581.2Syn Z: 0.91

ClinVar Variant Classifications

223 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7

Likely Pathogenic4

VUS151

Likely Benign26

Benign2

Conflicting1

Pathogenic

Likely Pathogenic

151

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	7	0	0	0	7
Likely Pathogenic	3	0	0	1	4
VUS	0	151	0	0	151
Likely Benign	0	13	0	13	26
Benign	0	1	1	0	2
Conflicting	—				1
Total	10	165	1	14	191

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

39 pathogenic / likely-pathogenic (of 42) ClinVar copy-number / structural variants overlap GOLGA2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →