AP3S2

adaptor related protein complex 3 subunit sigma 2, the group of Adaptor related protein complex 3|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:89830598-89894638

Links

ENSG00000157823 ∙ NCBI:10239 ∙ OMIM:602416 ∙ HGNC:571 ∙ Uniprot:P59780 ∙ 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 AP3S2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP3S2 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						0
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in AP3S2

This is a list of pathogenic ClinVar variants found in the AP3S2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-89835538-G-A		not specified	Uncertain significance (Sep 21, 2021)
15-89835627-G-A		not specified	Uncertain significance (Dec 28, 2023)
15-89837648-C-G		not specified	Uncertain significance (Apr 25, 2022)
15-89871516-C-T		not specified	Uncertain significance (Dec 14, 2023)
15-89888534-A-G		not specified	Uncertain significance (Jan 24, 2023)
15-89888588-G-A		not specified	Uncertain significance (Feb 22, 2023)
15-89893882-A-G		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP3S2	protein_coding	protein_coding	ENST00000336418	6	63744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000233	0.517	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0910	106	109	0.975	0.00000576	1280
Missense in Polyphen		27	31.409	0.85963		415
Synonymous	-0.888	47	39.9	1.18	0.00000203	357
Loss of Function	0.603	8	10.1	0.795	4.91e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000800	0.000799
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000548	0.0000544
South Asian	0.0000982	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of the AP-3 complex, an adaptor-related complex which is not clathrin-associated. The complex is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. In concert with the BLOC-1 complex, AP-3 is required to target cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals.
• Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.687
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

• pHI: 0.0819
• hipred: N
• hipred_score: 0.401
• ghis: 0.452

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Ap3s2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: intracellular protein transport;anterograde axonal transport;anterograde synaptic vesicle transport
• Cellular component: Golgi apparatus;AP-3 adaptor complex;cytoplasmic vesicle membrane;intracellular membrane-bounded organelle;axon cytoplasm