GOLGA3

golgin A3, the group of Golgins

Basic information

Region (hg38): 12:132768902-132829143

Links

ENSG00000090615 ∙ NCBI:2802 ∙ OMIM:602581 ∙ HGNC:4426 ∙ Uniprot:Q08378 ∙ 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 GOLGA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA3 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	2	8
missense			153	14	2	169
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	153	20	4

Variants in GOLGA3

This is a list of pathogenic ClinVar variants found in the GOLGA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132773119-C-T		not specified	Uncertain significance (May 10, 2024)
12-132773144-G-C		not specified	Uncertain significance (Dec 04, 2024)
12-132773160-C-T		not specified	Uncertain significance (Dec 02, 2024)
12-132773161-C-T		not specified	Uncertain significance (May 13, 2024)
12-132773163-C-T		not specified	Uncertain significance (May 16, 2022)
12-132773167-G-C		not specified	Uncertain significance (Oct 04, 2022)
12-132773176-G-T		not specified	Uncertain significance (Jan 20, 2025)
12-132773179-C-A		not specified	Uncertain significance (Jan 10, 2023)
12-132773184-G-A		not specified	Likely benign (Aug 02, 2021)
12-132773220-G-A		not specified	Uncertain significance (Sep 29, 2022)
12-132773226-G-A		not specified	Uncertain significance (Oct 11, 2024)
12-132773239-C-T		not specified	Uncertain significance (Jan 12, 2024)
12-132773242-G-A		not specified	Uncertain significance (Jan 17, 2024)
12-132773247-G-A		not specified	Uncertain significance (Jan 23, 2023)
12-132774182-G-A			Likely benign (Mar 01, 2024)
12-132774191-G-C		not specified	Uncertain significance (Nov 11, 2024)
12-132774206-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-132774213-C-T			Likely benign (Jan 01, 2023)
12-132774241-G-A		not specified	Uncertain significance (Apr 07, 2023)
12-132774277-G-A		not specified	Uncertain significance (Sep 13, 2023)
12-132774296-T-C		not specified	Uncertain significance (May 15, 2023)
12-132774302-C-T		not specified	Uncertain significance (Nov 25, 2024)
12-132775152-C-T		not specified	Uncertain significance (May 12, 2024)
12-132775155-C-T		not specified	Uncertain significance (Nov 09, 2023)
12-132775202-T-C		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA3	protein_coding	protein_coding	ENST00000204726	23	59950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00680	0.993	125656	0	92	125748	0.000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0549	878	883	0.995	0.0000564	9733
Missense in Polyphen		288	318.79	0.90341		3731
Synonymous	-1.15	437	408	1.07	0.0000300	2907
Loss of Function	5.98	20	76.4	0.262	0.00000398	839

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00147	0.00147
Finnish	0.0000954	0.0000924
European (Non-Finnish)	0.000191	0.000185
Middle Eastern	0.00147	0.00147
South Asian	0.000360	0.000359
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Golgi auto-antigen; probably involved in maintaining Golgi structure.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.462
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.97

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.579
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.829

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golga3
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: intra-Golgi vesicle-mediated transport;spermatogenesis
• Cellular component: Golgi membrane;nucleus;nucleoplasm;nucleolus;cytoplasm;Golgi apparatus;cytosol;membrane;Golgi transport complex;Golgi cisterna membrane;extrinsic component of Golgi membrane
• Molecular function: transporter activity;protein binding;cadherin binding