GGA2

golgi associated, gamma adaptin ear containing, ARF binding protein 2, the group of Golgi associated, gamma adaptin ear containing, ARF binding proteins

Basic information

Region (hg38): 16:23462213-23521995

Links

ENSG00000103365 ∙ NCBI:23062 ∙ OMIM:606005 ∙ HGNC:16064 ∙ Uniprot:Q9UJY4 ∙ 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 GGA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGA2 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	1		47
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	3	0

Variants in GGA2

This is a list of pathogenic ClinVar variants found in the GGA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23467604-A-C		not specified	Uncertain significance (Jun 10, 2022)
16-23467627-T-G		not specified	Uncertain significance (Jan 10, 2022)
16-23467657-C-G		not specified	Uncertain significance (Apr 26, 2023)
16-23467668-G-C		not specified	Uncertain significance (Sep 22, 2022)
16-23467668-G-T		not specified	Uncertain significance (Jun 06, 2023)
16-23467691-G-A		not specified	Uncertain significance (Mar 16, 2022)
16-23467694-T-C		not specified	Uncertain significance (Jan 03, 2022)
16-23470016-A-G		not specified	Uncertain significance (Nov 21, 2022)
16-23470025-C-A		not specified	Uncertain significance (Dec 06, 2023)
16-23470031-C-G		not specified	Uncertain significance (Oct 17, 2023)
16-23470045-G-A		not specified	Uncertain significance (Nov 20, 2023)
16-23470071-C-A		not specified	Uncertain significance (Aug 17, 2022)
16-23474929-A-T		not specified	Uncertain significance (Jun 29, 2023)
16-23475050-G-A		not specified	Uncertain significance (Apr 05, 2023)
16-23478377-G-A		not specified	Likely benign (Jun 07, 2024)
16-23478401-T-G		not specified	Uncertain significance (Jun 26, 2023)
16-23478894-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-23478900-C-T		not specified	Uncertain significance (Jul 20, 2021)
16-23479800-A-C		not specified	Uncertain significance (Nov 29, 2023)
16-23479806-G-A		not specified	Uncertain significance (Mar 30, 2024)
16-23479873-C-T		not specified	Likely benign (Oct 13, 2023)
16-23480650-G-A		not specified	Uncertain significance (Nov 15, 2021)
16-23480677-G-T		not specified	Uncertain significance (May 09, 2023)
16-23480681-C-T		not specified	Uncertain significance (Feb 06, 2024)
16-23480701-C-T		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGA2	protein_coding	protein_coding	ENST00000309859	17	58454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-7	0.998	125706	0	41	125747	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	327	335	0.977	0.0000184	3958
Missense in Polyphen		133	133.18	0.99866		1560
Synonymous	-0.222	136	133	1.02	0.00000777	1212
Loss of Function	2.71	17	34.0	0.500	0.00000160	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000164	0.000163
South Asian	0.000131	0.000131
Other	0.000326	0.000326

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.
• Pathway: Lysosome - Homo sapiens (human);Vesicle-mediated transport;TBC/RABGAPs;Membrane Trafficking;Metabolism of proteins;Amyloid fiber formation;Rab regulation of trafficking (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.834
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.85

Haploinsufficiency Scores

• pHI: 0.0779
• hipred: Y
• hipred_score: 0.637
• ghis: 0.624

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gga2
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region 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)

Gene ontology

• Biological process: intracellular protein transport;protein localization to cell surface;Golgi to plasma membrane protein transport;cellular protein metabolic process
• Cellular component: Golgi apparatus;trans-Golgi network;endosome membrane;clathrin-coated vesicle;early endosome membrane
• Molecular function: protein binding;ADP-ribosylation factor binding