AP1S2
Basic information
Region (hg38): X:15825806-15854931
Previous symbols: [ "MRX59", "MRXS5", "PGS" ]
Links
Phenotypes
GenCC
Source:
- syndromic X-linked intellectual disability 5 (Strong), mode of inheritance: XL
- syndromic X-linked intellectual disability 5 (Moderate), mode of inheritance: XL
- syndromic X-linked intellectual disability 5 (Supportive), mode of inheritance: XL
- fried syndrome (Supportive), mode of inheritance: XL
- autism spectrum disorder (Limited), mode of inheritance: XL
- syndromic X-linked intellectual disability 5 (Strong), mode of inheritance: XL
- X-linked syndromic intellectual disability (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Pettigrew syndrome | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 5054319; 10398241; 12599187; 17617514; 18428203; 19377476; 2018058; 22210230; 23756445 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (7 variants)
- Pettigrew syndrome (7 variants)
- Fried syndrome;Pettigrew syndrome (1 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AP1S2 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 | 10 | 13 | ||||
missense | 12 | 13 | ||||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
splice region | 1 | 1 | 1 | 3 | 6 | |
non coding | 21 | |||||
Total | 12 | 4 | 16 | 19 | 11 |
Variants in AP1S2
This is a list of pathogenic ClinVar variants found in the AP1S2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-15827084-T-G | Pettigrew syndrome | Uncertain significance (May 02, 2023) | ||
X-15827324-G-A | Inborn genetic diseases | Uncertain significance (Jan 26, 2017) | ||
X-15827326-T-C | Likely benign (Jul 25, 2023) | |||
X-15827328-T-C | Likely benign (Nov 19, 2021) | |||
X-15827335-C-T | Uncertain significance (Jul 11, 2022) | |||
X-15827336-C-T | Uncertain significance (Apr 07, 2020) | |||
X-15827377-G-A | not specified | Likely benign (Sep 29, 2017) | ||
X-15827389-TGA-T | Likely benign (Mar 15, 2021) | |||
X-15828209-G-T | not specified | Likely benign (Sep 16, 2015) | ||
X-15845153-T-C | Benign (May 10, 2021) | |||
X-15845173-T-C | Benign (May 10, 2021) | |||
X-15845186-A-G | Benign (May 10, 2021) | |||
X-15845364-G-C | Likely benign (Jun 29, 2023) | |||
X-15845370-G-A | Likely benign (Oct 24, 2024) | |||
X-15845378-C-A | Pettigrew syndrome | Pathogenic (Sep 26, 2013) | ||
X-15845389-A-C | Uncertain significance (Jan 22, 2024) | |||
X-15845405-T-C | Uncertain significance (Jul 30, 2024) | |||
X-15845419-T-A | Uncertain significance (Aug 22, 2022) | |||
X-15845419-T-G | Uncertain significance (Jun 23, 2024) | |||
X-15845432-T-G | Inborn genetic diseases | Uncertain significance (Aug 04, 2024) | ||
X-15845438-G-A | Pettigrew syndrome | Pathogenic (Oct 04, 2024) | ||
X-15845470-ATAAAATAAGCCTTC-A | Pettigrew syndrome | Likely pathogenic (Jun 04, 2020) | ||
X-15845485-TC-T | Pettigrew syndrome | Pathogenic (Apr 29, 2024) | ||
X-15845496-G-A | Likely benign (Aug 21, 2022) | |||
X-15845518-T-C | Pathogenic (Apr 21, 2016) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AP1S2 | protein_coding | protein_coding | ENST00000329235 | 4 | 29126 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.867 | 0.131 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.01 | 15 | 58.2 | 0.258 | 0.00000455 | 1027 |
Missense in Polyphen | 5 | 18.951 | 0.26384 | 361 | ||
Synonymous | -0.425 | 22 | 19.6 | 1.12 | 0.00000137 | 286 |
Loss of Function | 2.38 | 0 | 6.60 | 0.00 | 5.37e-7 | 112 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Subunit of clathrin-associated adaptor protein complex 1 that plays a role in protein sorting in the late-Golgi/trans-Golgi network (TGN) and/or endosomes. The AP complexes mediate both 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)
Recessive Scores
- pRec
- 0.0507
Intolerance Scores
- loftool
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.749
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.492
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.846
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Low | Low | Low |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Ap1s2
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- intracellular protein transport;vesicle-mediated transport;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;Golgi apparatus;cytosol;clathrin-coated pit;AP-type membrane coat adaptor complex;cytoplasmic vesicle membrane;trans-Golgi network membrane;intracellular membrane-bounded organelle
- Molecular function
- protein binding