GOLGB1

golgin B1, the group of Golgins

Basic information

Region (hg38): 3:121663199-121749966

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.

not_specified (372 variants)
not_provided (9 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. These statistics are base on transcript: NM_001366282.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar		6
missense			352 clinvar	21 clinvar	2 clinvar	375
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	352	27	2

Loading clinvar variants...

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