GOLGB1

Chr 3

golgin B1

Also known as: GCP, GCP372, GOLIM1

NCBI Gene: 2804 ENSG00000173230 UniProt: Q14789 OMIM: 602500

The GOLGB1 protein enables RNA binding and participates in forming intercisternal cross-bridges of the Golgi complex, with involvement in protein localization to pericentriolar material. Mutations cause autosomal recessive intellectual disability with microcephaly and seizures, typically presenting in early childhood. This gene is highly constrained against loss-of-function variants, indicating its critical importance for normal cellular function.

OMIM ResearchSummary from RefSeq, UniProt

Enables RNA binding activity. Involved in protein localization to pericentriolar material. Located in Golgi apparatus and endoplasmic reticulum-Golgi intermediate compartment. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.42

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.42LOEUF

pLI 0.000

Z-score 7.48

OE 0.33 (0.26–0.42)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.29Z-score

OE missense 0.91 (0.87–0.95)

1397 obs / 1539.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.33 (0.26–0.42)

0≤0.351.4

Missense OE?0.91 (0.87–0.95)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 48 / 145.3Missense obs/exp: 1397 / 1539.4Syn Z: 0.55

Background carrier burden — how many people carry a rare variant somewhere in GOLGB1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 17

3,592 rare PASS variants

Rare truncating (LoF)

1 in 610

395 rare PASS variants

Rare synonymous (reference)

1 in 44

1,303 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GOLGB1. 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 24	1 in 620
South Asian	~43k	1 in 16	1 in 600
Remaining (unassigned)	~30k	1 in 15	1 in 320
European (Finnish)	~27k	1 in 53	1 in 1,400
Admixed American	~22k	1 in 16	1 in 370
African / African American	~21k	1 in 17	1 in 360
East Asian	~20k	1 in 18	1 in 460
Ashkenazi Jewish	~13k	1 in 100	1 in 390
Middle Eastern	~2,884	1 in 22	1 in 570

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 13 of 21 coding exons well covered in gnomAD exomes; exons 5, 6, 11, 12, 15 and 3 more marginal. Genomes: all 21.? see exons ↓