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.

not_specified (96 variants)
not_provided (3 variants)

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. These statistics are base on transcript: NM_000015044.4. 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				3 clinvar		3
missense			93 clinvar	3 clinvar		96
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	6	0

Loading clinvar variants...

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