GGA3

golgi associated, gamma adaptin ear containing, ARF binding protein 3, the group of Golgi associated, gamma adaptin ear containing, ARF binding proteins

Basic information

Region (hg38): 17:75236598-75262363

Links

ENSG00000125447 ∙ NCBI:23163 ∙ OMIM:606006 ∙ HGNC:17079 ∙ Uniprot:Q9NZ52 ∙ 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 GGA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGA3 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					2	2
missense			46	4	1	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	4	3

Variants in GGA3

This is a list of pathogenic ClinVar variants found in the GGA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75238289-C-T		not specified	Uncertain significance (Jul 20, 2022)
17-75238323-C-T		not specified	Uncertain significance (Jun 27, 2023)
17-75238653-T-G		not specified	Uncertain significance (Jun 22, 2021)
17-75238698-G-A		not specified	Uncertain significance (Mar 25, 2024)
17-75238705-T-G		not specified	Uncertain significance (Sep 27, 2022)
17-75238747-A-G			Benign (May 14, 2018)
17-75238945-T-C		not specified	Uncertain significance (Jun 16, 2024)
17-75238984-A-G		not specified	Uncertain significance (Feb 28, 2024)
17-75239002-C-T		not specified	Uncertain significance (Mar 31, 2023)
17-75239018-C-G		not specified	Uncertain significance (Apr 28, 2022)
17-75239057-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-75239075-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-75239431-T-C		not specified	Uncertain significance (Aug 12, 2022)
17-75239435-G-C		not specified	Uncertain significance (Oct 05, 2022)
17-75239457-A-T		not specified	Uncertain significance (Dec 03, 2021)
17-75239491-G-A		not specified	Uncertain significance (Jun 22, 2024)
17-75239516-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-75239537-G-C		not specified	Uncertain significance (Dec 01, 2022)
17-75239810-T-C		not specified	Uncertain significance (Jan 31, 2024)
17-75239838-C-T		not specified	Likely benign (May 04, 2022)
17-75239847-C-G		not specified	Uncertain significance (Jan 30, 2024)
17-75239853-C-T		not specified	Uncertain significance (Mar 24, 2023)
17-75239900-G-A		not specified	Uncertain significance (Oct 14, 2023)
17-75239936-G-A		not specified	Likely benign (Sep 27, 2022)
17-75239952-C-T		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGA3	protein_coding	protein_coding	ENST00000245541	17	25751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000167	0.999	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0105	413	412	1.00	0.0000236	4637
Missense in Polyphen		145	173.39	0.83626		1976
Synonymous	-0.952	199	183	1.09	0.0000119	1478
Loss of Function	2.80	15	32.1	0.467	0.00000143	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.000325	0.000298
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes. Mediates the ARF- dependent recruitment of clathrin to the TGN and binds ubiquitinated proteins and membrane cargo molecules with a cytosolic acidic cluster-dileucine (AC-LL) motif. {ECO:0000269|PubMed:11301005}.
• Pathway: Lysosome - Homo sapiens (human);Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Metabolism of proteins;Amyloid fiber formation;Rab regulation of trafficking;Arf1 pathway (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.71

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.379
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gga3
• Phenotype: reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: intracellular protein transport;regulation of protein stability;protein destabilization;endocytic recycling;protein localization to cell surface;Golgi to plasma membrane protein transport;cellular protein metabolic process;positive regulation of protein catabolic process;protein localization to lysosome;negative regulation of amyloid-beta formation
• Cellular component: Golgi apparatus;trans-Golgi network;endosome membrane;early endosome membrane;recycling endosome membrane
• Molecular function: protein binding;ADP-ribosylation factor binding;ubiquitin binding