AP1M1

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

Basic information

Region (hg38): 19:16197854-16245906

Links

ENSG00000072958NCBI:8907OMIM:603535HGNC:13667Uniprot:Q9BXS5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AP1M1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1M1 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
2
clinvar
2
missense
20
clinvar
20
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 20 2 0

Variants in AP1M1

This is a list of pathogenic ClinVar variants found in the AP1M1 region.

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

Position Type Phenotype Significance ClinVar
19-16198064-G-T not specified Uncertain significance (Jan 10, 2023)2474855
19-16203481-G-A not specified Uncertain significance (Mar 07, 2024)3127463
19-16203573-G-A not specified Uncertain significance (Feb 12, 2025)3876586
19-16206365-C-T not specified Uncertain significance (Jun 25, 2024)3403399
19-16206370-G-A not specified Uncertain significance (Apr 23, 2024)3300368
19-16206390-C-A not specified Uncertain significance (May 18, 2022)2290085
19-16208038-A-G not specified Uncertain significance (Dec 10, 2024)3403388
19-16208061-C-T not specified Uncertain significance (Dec 15, 2023)3127462
19-16208093-G-C Likely benign (Mar 01, 2023)2649508
19-16208118-C-T not specified Uncertain significance (Feb 06, 2023)2481073
19-16208146-A-G not specified Uncertain significance (Dec 16, 2022)2397037
19-16209074-G-A not specified Uncertain significance (Nov 08, 2024)3403438
19-16209125-A-G not specified Uncertain significance (Mar 27, 2023)2524600
19-16226445-C-T not specified Uncertain significance (Oct 11, 2024)3403409
19-16226470-A-G not specified Uncertain significance (May 15, 2024)3300356
19-16227611-G-A not specified Uncertain significance (Apr 13, 2022)2283737
19-16227688-C-T not specified Uncertain significance (Aug 14, 2024)3403419
19-16228152-T-C not specified Uncertain significance (Mar 22, 2023)2528533
19-16228809-G-A not specified Uncertain significance (Feb 27, 2024)2272788
19-16228861-C-T not specified Uncertain significance (Oct 12, 2024)3403429
19-16228898-C-T Likely benign (Mar 01, 2023)2649509
19-16233526-G-A not specified Uncertain significance (Aug 05, 2023)2588323
19-16234254-G-A not specified Uncertain significance (Jun 01, 2023)2555106

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
AP1M1protein_codingprotein_codingENST00000444449 1337772
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7130.2871257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.701162950.3940.00002012851
Missense in Polyphen34134.570.252661280
Synonymous0.3091201240.9650.00000938813
Loss of Function3.82526.00.1920.00000139283

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00009400.0000924
European (Non-Finnish)0.00006160.0000615
Middle Eastern0.000.00
South Asian0.00009960.0000980
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the trans-Golgi network (TGN) and endosomes. The AP complexes mediate the recruitment of clathrin to membranes and the recognition of sorting signals within the cytosolic tails of transmembrane cargo molecules.;
Pathway
Lysosome - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;Disease;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Host Interactions of HIV factors;HIV Infection;MHC class II antigen presentation;Infectious disease;Innate Immune System;Immune System;Adaptive Immune System;Nef mediated downregulation of MHC class I complex cell surface expression;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;E-cadherin signaling in the nascent adherens junction (Consensus)

Recessive Scores

pRec
0.178

Intolerance Scores

loftool
0.467
rvis_EVS
-0.87
rvis_percentile_EVS
10.65

Haploinsufficiency Scores

pHI
0.420
hipred
Y
hipred_score
0.825
ghis
0.627

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.812

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ap1m1
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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
ap1m1
Affected structure
midbrain hindbrain boundary
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

Biological process
intracellular protein transport;antigen processing and presentation of exogenous peptide antigen via MHC class II;melanosome organization;endosome to melanosome transport;neutrophil degranulation;regulation of defense response to virus by virus
Cellular component
Golgi membrane;lysosomal membrane;cytosol;plasma membrane;membrane;clathrin adaptor complex;cytoplasmic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane;specific granule membrane;extracellular exosome
Molecular function
protein binding