GOLGA1

golgin A1, the group of Golgins

Basic information

Region (hg38): 9:124878275-124948492

Links

ENSG00000136935 ∙ NCBI:2800 ∙ OMIM:602502 ∙ HGNC:4424 ∙ Uniprot:Q92805 ∙ 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 GOLGA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA1 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				1	2	3
missense			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	29	4	2

Variants in GOLGA1

This is a list of pathogenic ClinVar variants found in the GOLGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-124880535-A-G		not specified	Uncertain significance (Jun 16, 2024)
9-124880547-G-A		not specified	Uncertain significance (Mar 20, 2023)
9-124880579-T-C		not specified	Uncertain significance (Oct 27, 2022)
9-124880597-C-G		not specified	Uncertain significance (Jun 03, 2022)
9-124881207-C-G		not specified	Uncertain significance (Apr 12, 2024)
9-124881885-G-A		not specified	Uncertain significance (Oct 02, 2023)
9-124881899-A-G		not specified	Uncertain significance (Jul 26, 2022)
9-124881900-T-A		not specified	Uncertain significance (May 12, 2024)
9-124881920-C-T		not specified	Uncertain significance (Apr 07, 2022)
9-124888295-C-G		not specified	Uncertain significance (Nov 17, 2023)
9-124888352-A-C			Benign (Dec 31, 2019)
9-124888380-A-G		not specified	Uncertain significance (Aug 12, 2024)
9-124889147-G-A		not specified	Uncertain significance (Jun 16, 2024)
9-124889170-G-A			Benign (Jun 04, 2018)
9-124889186-C-T		not specified	Likely benign (Aug 05, 2024)
9-124889223-C-T		not specified	Uncertain significance (Oct 30, 2024)
9-124889256-C-G		not specified	Uncertain significance (Jun 29, 2022)
9-124889260-C-G		not specified	Uncertain significance (Apr 05, 2024)
9-124889263-G-A		not specified	Likely benign (Jan 30, 2024)
9-124889297-T-C		not specified	Uncertain significance (Aug 04, 2023)
9-124889436-C-T		not specified	Likely benign (Oct 08, 2024)
9-124889479-C-T		not specified	Uncertain significance (Feb 02, 2024)
9-124889481-G-T		not specified	Uncertain significance (Mar 31, 2024)
9-124889482-T-C		not specified	Uncertain significance (Jan 11, 2023)
9-124889490-C-T		not specified	Likely benign (Jun 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA1	protein_coding	protein_coding	ENST00000373555	21	70126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000143	1.00	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	339	412	0.823	0.0000227	5028
Missense in Polyphen		90	131.95	0.68205		1690
Synonymous	1.04	142	159	0.895	0.00000895	1383
Loss of Function	4.27	20	53.7	0.372	0.00000276	605

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000164	0.000163
South Asian	0.000363	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in vesicular trafficking at the Golgi apparatus level. Involved in endosome-to-Golgi trafficking. {ECO:0000269|PubMed:29084197}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.79

Haploinsufficiency Scores

• pHI: 0.642
• hipred: N
• hipred_score: 0.492
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.789

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golga1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Cellular component: Golgi membrane;acrosomal vesicle;Golgi apparatus;trans-Golgi network;cytosol;perinuclear region of cytoplasm
• Molecular function: protein binding