GOLGB1

golgin B1, the group of Golgins

Basic information

Region (hg38): 3:121663198-121749966

Links

ENSG00000173230 ∙ NCBI:2804 ∙ OMIM:602500 ∙ HGNC:4429 ∙ Uniprot:Q14789 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GOLGB1 gene.

• Inborn genetic diseases (112 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGB1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6		6
missense			109	4	1	114
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	109	10	1

Variants in GOLGB1

This is a list of pathogenic ClinVar variants found in the GOLGB1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-121664536-T-C		not specified	Uncertain significance (Nov 02, 2023)
3-121664556-C-T		not specified	Uncertain significance (Jun 09, 2022)
3-121664563-G-A		not specified	Uncertain significance (Dec 09, 2023)
3-121664945-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-121664945-G-C		not specified	Uncertain significance (Oct 21, 2021)
3-121664960-A-C		not specified	Uncertain significance (Dec 27, 2023)
3-121664987-C-G		not specified	Uncertain significance (Apr 13, 2022)
3-121667477-G-A		not specified	Uncertain significance (Aug 16, 2022)
3-121667482-A-T		not specified	Uncertain significance (Mar 08, 2024)
3-121667530-T-A		not specified	Uncertain significance (Jun 11, 2021)
3-121667567-C-T		not specified	Likely benign (Jan 24, 2024)
3-121668142-T-C		not specified	Uncertain significance (Jun 29, 2023)
3-121669213-G-A		not specified	Uncertain significance (May 09, 2023)
3-121669232-G-C		not specified	Uncertain significance (Jun 24, 2022)
3-121669247-C-A		not specified	Uncertain significance (Dec 06, 2022)
3-121669294-C-T		not specified	Uncertain significance (Jan 30, 2024)
3-121676985-C-A		not specified	Uncertain significance (May 17, 2023)
3-121677012-C-G		not specified	Uncertain significance (Mar 29, 2023)
3-121677369-C-A		not specified	Uncertain significance (Dec 01, 2022)
3-121677412-A-G		not specified	Uncertain significance (Oct 05, 2021)
3-121677426-T-C		not specified	Uncertain significance (Aug 03, 2022)
3-121690676-G-T		not specified	Uncertain significance (Mar 29, 2022)
3-121690850-G-T			Likely benign (Jan 31, 2018)
3-121690985-G-A			Likely benign (May 01, 2022)
3-121691014-T-C		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGB1	protein_coding	protein_coding	ENST00000393667	21	86557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.30e-12	1.00	125615	0	133	125748	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	1397	1.54e+3	0.907	0.0000748	21823
Missense in Polyphen		383	469.53	0.8157		7256
Synonymous	0.551	554	571	0.971	0.0000278	5782
Loss of Function	7.48	48	145	0.330	0.00000734	1875

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.000421	0.000397
East Asian	0.000991	0.000925
Finnish	0.000418	0.000416
European (Non-Finnish)	0.000469	0.000466
Middle Eastern	0.000991	0.000925
South Asian	0.000625	0.000523
Other	0.00117	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in forming intercisternal cross-bridges of the Golgi complex.
• Pathway: Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-mediated anterograde transport;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.841
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.77

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.289
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Golgb1
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: golgb1
• Affected structure: ciliated olfactory receptor neuron
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: regulation of transcription, DNA-templated;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;protein localization to pericentriolar material
• Cellular component: Golgi membrane;endoplasmic reticulum-Golgi intermediate compartment;Golgi apparatus;Golgi stack;cis-Golgi network;membrane;integral component of membrane
• Molecular function: DNA-binding transcription factor activity;RNA binding;protein binding;sequence-specific DNA binding