AP1M2
adaptor related protein complex 1 subunit mu 2, the group of Adaptor related protein complex 1
Basic information
Region (hg38): 19:10572671-10587315
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1M2 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 | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 25 | 0 | 0 |
Variants in AP1M2
This is a list of pathogenic ClinVar variants found in the AP1M2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-10574453-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 19-10574483-T-G | not specified | Uncertain significance (Jan 27, 2022) | ||
| 19-10574953-G-C | not specified | Uncertain significance (Nov 30, 2022) | ||
| 19-10574956-G-T | not specified | Uncertain significance (Sep 25, 2023) | ||
| 19-10575029-C-T | not specified | Uncertain significance (Jul 11, 2023) | ||
| 19-10577202-A-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 19-10577253-C-G | not specified | Uncertain significance (Nov 18, 2022) | ||
| 19-10577320-C-T | not specified | Likely benign (Jun 17, 2024) | ||
| 19-10579781-G-A | not specified | Uncertain significance (May 29, 2024) | ||
| 19-10581286-A-C | not specified | Uncertain significance (Sep 07, 2022) | ||
| 19-10581287-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 19-10581353-C-T | not specified | Uncertain significance (Jun 29, 2022) | ||
| 19-10581380-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
| 19-10581545-C-T | not specified | Uncertain significance (Feb 12, 2024) | ||
| 19-10581560-G-T | not specified | Uncertain significance (Jan 09, 2024) | ||
| 19-10581584-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
| 19-10581588-C-T | not specified | Uncertain significance (Nov 14, 2023) | ||
| 19-10581590-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
| 19-10581591-G-A | not specified | Uncertain significance (Jan 17, 2024) | ||
| 19-10581792-C-G | not specified | Uncertain significance (Feb 05, 2024) | ||
| 19-10581835-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
| 19-10583943-A-C | not specified | Uncertain significance (Jan 17, 2024) | ||
| 19-10583957-G-C | not specified | Uncertain significance (Nov 13, 2023) | ||
| 19-10584043-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 19-10584058-G-A | not specified | Uncertain significance (Jan 03, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AP1M2 | protein_coding | protein_coding | ENST00000250244 | 12 | 14645 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 2.14e-8 | 0.690 | 125603 | 0 | 139 | 125742 | 0.000553 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.676 | 223 | 253 | 0.880 | 0.0000154 | 2747 |
| Missense in Polyphen | 80 | 102.81 | 0.77812 | 1181 | ||
| Synonymous | -0.589 | 110 | 102 | 1.07 | 0.00000695 | 780 |
| Loss of Function | 1.29 | 15 | 21.5 | 0.699 | 9.81e-7 | 267 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000539 | 0.000534 |
| Ashkenazi Jewish | 0.000103 | 0.0000992 |
| East Asian | 0.000286 | 0.000217 |
| Finnish | 0.000375 | 0.000370 |
| European (Non-Finnish) | 0.000769 | 0.000756 |
| Middle Eastern | 0.000286 | 0.000217 |
| South Asian | 0.000695 | 0.000686 |
| Other | 0.000499 | 0.000489 |
dbNSFP
Source:
- 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;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;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
(Consensus)
Intolerance Scores
- loftool
- 0.755
- rvis_EVS
- -0.87
- rvis_percentile_EVS
- 10.73
Haploinsufficiency Scores
- pHI
- 0.558
- hipred
- Y
- hipred_score
- 0.646
- ghis
- 0.566
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.680
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ap1m2
- 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); digestive/alimentary phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- ap1m2
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- kinked
Gene ontology
- Biological process
- protein targeting;vesicle targeting;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of defense response to virus by virus
- Cellular component
- Golgi membrane;lysosomal membrane;cytosol;clathrin adaptor complex;cytoplasmic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane;intracellular membrane-bounded organelle
- Molecular function
- protein binding