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…

DNmechanismLOEUF 0.42

Clinical Summary— GOLGB1

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 387 VUS of 445 total submissions

Explore recent and relevant literature in Research Assistant →

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

This gene — mechanism propensity

0.74top 25%

GOF

0.4777th %ile

LOF

0.2872th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

445 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

VUS387

Likely Benign27

Benign2

Pathogenic

387

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	1	0	1
Likely Pathogenic	0	0	0	0	0
VUS	1	386	0	0	387
Likely Benign	0	21	0	6	27
Benign	0	2	0	0	2
Total	1	409	1	6	417

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

View in ClinVar →

18 pathogenic / likely-pathogenic (of 20) ClinVar copy-number / structural variants overlap GOLGB1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →