AP3M1

adaptor related protein complex 3 subunit mu 1, the group of Adaptor related protein complex 3

Basic information

Region (hg38): 10:74120255-74150842

Links

ENSG00000185009 ∙ NCBI:26985 ∙ OMIM:610366 ∙ HGNC:569 ∙ Uniprot:Q9Y2T2 ∙ 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 AP3M1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP3M1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in AP3M1

This is a list of pathogenic ClinVar variants found in the AP3M1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-74123901-A-G		not specified	Uncertain significance (Nov 07, 2022)
10-74124413-T-G		not specified	Uncertain significance (Apr 22, 2022)
10-74124439-T-C		not specified	Uncertain significance (Jan 06, 2023)
10-74124451-G-A		not specified	Uncertain significance (Oct 26, 2022)
10-74126170-T-C		not specified	Uncertain significance (Feb 15, 2023)
10-74126294-C-A		not specified	Uncertain significance (Jul 20, 2021)
10-74126303-T-A		not specified	Uncertain significance (Jun 24, 2022)
10-74126338-A-G		not specified	Uncertain significance (Aug 28, 2023)
10-74126345-T-C		not specified	Uncertain significance (Oct 26, 2022)
10-74129184-C-T		not specified	Uncertain significance (Feb 23, 2023)
10-74129189-C-T		not specified	Uncertain significance (Feb 10, 2023)
10-74129190-G-A		not specified	Uncertain significance (Jan 10, 2023)
10-74134104-C-T		not specified	Uncertain significance (Nov 21, 2023)
10-74134108-G-A		not specified	Uncertain significance (Sep 14, 2022)
10-74136765-A-C		not specified	Uncertain significance (Sep 17, 2021)
10-74138145-C-A		not specified	Uncertain significance (Feb 03, 2022)
10-74138198-C-T		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AP3M1	protein_coding	protein_coding	ENST00000355264	8	29298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0265	0.971	125725	0	21	125746	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	180	233	0.773	0.0000123	2756
Missense in Polyphen		38	66.478	0.57162		737
Synonymous	-0.372	84	79.8	1.05	0.00000409	802
Loss of Function	2.68	6	18.4	0.326	9.27e-7	223

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.0000333	0.0000327
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);Metabolism of proteins;Chaperonin-mediated protein folding;Association of TriC/CCT with target proteins during biosynthesis;Protein folding (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.591
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.239
• hipred: Y
• hipred_score: 0.696
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ap3m1

Gene ontology

• Biological process: protein targeting to lysosome;anterograde axonal transport;viral process;anterograde synaptic vesicle transport
• Cellular component: lysosome;lysosomal membrane;Golgi apparatus;clathrin adaptor complex;cytoplasmic vesicle membrane;axon cytoplasm
• Molecular function: protein binding;Rab GTPase binding