AP1G2

adaptor related protein complex 1 subunit gamma 2, the group of Clathrin/coatomer adaptor, adaptin-like, N-terminal domain containing|Adaptor related protein complex 1

Basic information

Region (hg38): 14:23559565-23568070

Links

ENSG00000213983 ∙ NCBI:8906 ∙ OMIM:603534 ∙ HGNC:556 ∙ Uniprot:O75843 ∙ 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 AP1G2 gene.

• not_specified (113 variants)
• Esophageal_atresia/tracheoesophageal_fistula (1 variants)
• Global_developmental_delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1G2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003917.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense		1	108	6		115
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	108	6	0

Highest pathogenic variant AF is 0.0000539169

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP1G2	protein_coding	protein_coding	ENST00000308724	21	8506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.10e-28	0.000286	125090	2	656	125748	0.00262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.391	449	473	0.949	0.0000273	5042
Missense in Polyphen		185	187.49	0.98669		2124
Synonymous	1.02	167	185	0.905	0.00000955	1691
Loss of Function	0.267	43	44.9	0.957	0.00000263	435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00474	0.00473
Ashkenazi Jewish	0.00377	0.00378
East Asian	0.00110	0.00109
Finnish	0.00102	0.00102
European (Non-Finnish)	0.00334	0.00330
Middle Eastern	0.00110	0.00109
South Asian	0.00186	0.00183
Other	0.00376	0.00375

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in protein sorting in late endosomes or multivesucular bodies (MVBs). {ECO:0000269|PubMed:9733768}.
• Pathway: Lysosome - Homo sapiens (human);Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking (Consensus)

Recessive Scores

• pRec: 0.0972

Intolerance Scores

• loftool: 0.976
• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.52

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.442
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.911

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap1g2

Zebrafish Information Network

• Gene name: ap1g2
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: intracellular protein transport;viral process;vesicle-mediated transport
• Cellular component: Golgi membrane;Golgi apparatus;Golgi-associated vesicle;endosome membrane;membrane;AP-1 adaptor complex;transport vesicle
• Molecular function: protein binding