AP3M2

adaptor related protein complex 3 subunit mu 2, the group of Adaptor related protein complex 3

Basic information

Region (hg38): 8:42152946-42171673

Links

ENSG00000070718 ∙ NCBI:10947 ∙ OMIM:610469 ∙ HGNC:570 ∙ Uniprot:P53677 ∙ 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 AP3M2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP3M2 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in AP3M2

This is a list of pathogenic ClinVar variants found in the AP3M2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42154711-C-G		not specified	Uncertain significance (Aug 21, 2024)
8-42154785-T-C		not specified	Uncertain significance (Nov 20, 2024)
8-42154830-T-C		not specified	Uncertain significance (May 29, 2024)
8-42154850-T-C		not specified	Uncertain significance (Jun 16, 2023)
8-42154913-C-G		not specified	Uncertain significance (Mar 11, 2022)
8-42154920-T-G		not specified	Uncertain significance (Jun 04, 2024)
8-42154941-G-A		not specified	Uncertain significance (Sep 30, 2024)
8-42158082-A-G		not specified	Uncertain significance (Jun 26, 2024)
8-42162295-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-42162338-G-A		not specified	Uncertain significance (May 28, 2024)
8-42165083-C-T		not specified	Uncertain significance (Aug 11, 2022)
8-42165149-C-G		not specified	Uncertain significance (Aug 28, 2023)
8-42165427-A-G		not specified	Uncertain significance (Oct 06, 2023)
8-42165484-G-C		not specified	Uncertain significance (Mar 06, 2023)
8-42165498-C-G		not specified	Uncertain significance (Feb 06, 2023)
8-42165529-C-T		not specified	Uncertain significance (Jan 09, 2024)
8-42167174-A-G		not specified	Uncertain significance (Jul 15, 2021)
8-42167208-G-A		not specified	Uncertain significance (Jan 02, 2024)
8-42167223-T-C		not specified	Uncertain significance (Aug 28, 2024)
8-42167228-C-T		not specified	Uncertain significance (Dec 21, 2022)
8-42167229-G-A		not specified	Uncertain significance (Aug 04, 2024)
8-42167257-G-T		not specified	Uncertain significance (May 15, 2023)
8-42167274-T-C		not specified	Uncertain significance (Jan 30, 2024)
8-42167345-A-G		not specified	Uncertain significance (May 05, 2023)
8-42167346-C-G		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP3M2	protein_coding	protein_coding	ENST00000518421	8	18728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-7	0.689	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	181	242	0.748	0.0000132	2759
Missense in Polyphen		60	85.811	0.69921		962
Synonymous	-0.356	92	87.8	1.05	0.00000466	829
Loss of Function	1.20	13	18.6	0.699	0.00000102	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000467	0.000467
Ashkenazi Jewish	0.000893	0.000893
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.000435	0.000435
South Asian	0.000233	0.000229
Other	0.00	0.00

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: 0.0942

Intolerance Scores

• loftool: 0.923
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.0667
• hipred: N
• hipred_score: 0.411
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap3m2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

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