GGA1

golgi associated, gamma adaptin ear containing, ARF binding protein 1, the group of Golgi associated, gamma adaptin ear containing, ARF binding proteins

Basic information

Region (hg38): 22:37608474-37633564

Links

ENSG00000100083 ∙ NCBI:26088 ∙ OMIM:606004 ∙ HGNC:17842 ∙ Uniprot:Q9UJY5 ∙ 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 GGA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGA1 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					3	3
missense			37	4		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	4	3

Variants in GGA1

This is a list of pathogenic ClinVar variants found in the GGA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37608900-A-G		not specified	Uncertain significance (Sep 10, 2024)
22-37614222-G-A		not specified	Likely benign (Nov 08, 2022)
22-37614238-A-G		not specified	Uncertain significance (Nov 22, 2023)
22-37614261-G-A		not specified	Uncertain significance (Apr 09, 2024)
22-37614267-T-G		not specified	Uncertain significance (May 31, 2023)
22-37616926-C-G		not specified	Uncertain significance (Jun 06, 2023)
22-37616939-G-A		not specified	Uncertain significance (Jul 20, 2021)
22-37618475-G-A		not specified	Uncertain significance (Apr 25, 2022)
22-37620289-C-G		not specified	Uncertain significance (Mar 14, 2023)
22-37620297-C-G		not specified	Uncertain significance (Mar 15, 2024)
22-37620316-G-A		not specified	Uncertain significance (Aug 15, 2023)
22-37620834-A-G		not specified	Uncertain significance (Jun 24, 2022)
22-37620842-G-A		not specified	Uncertain significance (Jan 02, 2024)
22-37620858-C-A		not specified	Uncertain significance (Apr 07, 2022)
22-37620860-C-T		not specified	Uncertain significance (May 31, 2023)
22-37621616-A-C		not specified	Uncertain significance (Oct 08, 2024)
22-37623441-G-C		not specified	Uncertain significance (Nov 25, 2024)
22-37623452-C-G		not specified	Uncertain significance (Aug 08, 2023)
22-37623565-G-A		not specified	Uncertain significance (Mar 28, 2023)
22-37624987-A-T		not specified	Uncertain significance (Nov 22, 2023)
22-37625049-G-A		not specified	Uncertain significance (Dec 15, 2022)
22-37625064-G-A		not specified	Uncertain significance (Jan 19, 2022)
22-37625875-G-A		not specified	Likely benign (Aug 13, 2021)
22-37625882-C-T			Benign (Jul 23, 2018)
22-37625898-G-A		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGA1	protein_coding	protein_coding	ENST00000343632	17	25091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000829	125718	0	8	125726	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	323	391	0.826	0.0000246	4129
Missense in Polyphen		104	143.28	0.72585		1526
Synonymous	-0.151	172	170	1.01	0.0000116	1287
Loss of Function	5.00	1	31.1	0.0322	0.00000141	367

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

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 (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.364
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.83

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.783
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gga1
• 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); reproductive system phenotype; hearing/vestibular/ear phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;protein localization;protein localization to cell surface;retrograde transport, endosome to Golgi;Golgi to plasma membrane protein transport;cellular protein metabolic process;positive regulation of protein catabolic process;toxin transport;protein localization to ciliary membrane
• Cellular component: nucleoplasm;early endosome;Golgi apparatus;cytosol;endosome membrane;membrane;early endosome membrane;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: molecular_function;protein binding;ADP-ribosylation factor binding;protein heterodimerization activity