AMER1
APC membrane recruitment protein 1, the group of APC membrane recruitment proteins
Basic information
Region (hg38): X:64185117-64205708
Previous symbols: [ "FAM123B" ]
Links
Phenotypes
GenCC
Source:
- osteopathia striata with cranial sclerosis (Strong), mode of inheritance: XL
- osteopathia striata with cranial sclerosis (Definitive), mode of inheritance: XL
- osteopathia striata with cranial sclerosis (Supportive), mode of inheritance: XL
- osteopathia striata with cranial sclerosis (Strong), mode of inheritance: XL
- osteopathia striata with cranial sclerosis (Strong), mode of inheritance: XL
- osteopathia striata with cranial sclerosis (Definitive), mode of inheritance: XL
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Osteopathia striata with cranial sclerosis | 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 | Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic | 19079258; 20209645; 20950377; 22987541 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (450 variants)
- Inborn_genetic_diseases (98 variants)
- Osteopathia_striata_with_cranial_sclerosis (56 variants)
- not_specified (31 variants)
- AMER1-related_disorder (29 variants)
- Intellectual_disability (4 variants)
- Colorectal_cancer (4 variants)
- Spinocerebellar_ataxia,_X-linked (1 variants)
- Obesity (1 variants)
- Ventriculomegaly (1 variants)
- Myocarditis (1 variants)
- Cleft_palate (1 variants)
- Febrile_seizure_(within_the_age_range_of_3_months_to_6_years) (1 variants)
- Macrocephaly (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMER1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152424.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 88 | 26 | 115 | |||
| missense | 246 | 83 | 40 | 369 | ||
| nonsense | 11 | 11 | 26 | |||
| start loss | 1 | 1 | ||||
| frameshift | 17 | 33 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 28 | 12 | 266 | 171 | 67 |
Highest pathogenic variant AF is 9.25837e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AMER1 | protein_coding | protein_coding | ENST00000330258 | 1 | 20628 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.854 | 0.146 | 125690 | 2 | 6 | 125698 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.569 | 474 | 440 | 1.08 | 0.0000330 | 7382 |
| Missense in Polyphen | 105 | 126.38 | 0.83083 | 2172 | ||
| Synonymous | -1.15 | 181 | 162 | 1.11 | 0.0000114 | 2325 |
| Loss of Function | 4.06 | 5 | 28.3 | 0.177 | 0.00000266 | 424 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000112 | 0.000112 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000738 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000497 | 0.0000352 |
| Middle Eastern | 0.0000738 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulator of the canonical Wnt signaling pathway. Acts by specifically binding phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), translocating to the cell membrane and interacting with key regulators of the canonical Wnt signaling pathway, such as components of the beta-catenin destruction complex. Acts both as a positive and negative regulator of the Wnt signaling pathway, depending on the context: acts as a positive regulator by promoting LRP6 phosphorylation. Also acts as a negative regulator by acting as a scaffold protein for the beta- catenin destruction complex and promoting stabilization of Axin at the cell membrane. Promotes CTNNB1 ubiquitination and degradation. Involved in kidney development. {ECO:0000269|PubMed:17510365, ECO:0000269|PubMed:17925383, ECO:0000269|PubMed:19416806, ECO:0000269|PubMed:21304492, ECO:0000269|PubMed:21498506}.;
- Pathway
- Degradation of beta-catenin by the destruction complex;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;Disassembly of the destruction complex and recruitment of AXIN to the membrane;Beta-catenin phosphorylation cascade;TCF dependent signaling in response to WNT
(Consensus)
Recessive Scores
- pRec
- 0.0852
Intolerance Scores
- loftool
- rvis_EVS
- -0.39
- rvis_percentile_EVS
- 27.03
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.734
- ghis
- 0.470
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amer1
- Phenotype
- embryo 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); hematopoietic system phenotype; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- amer1
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- Wnt signaling pathway;positive regulation of protein ubiquitination;bone development;adipose tissue development;regulation of canonical Wnt signaling pathway;mesenchymal cell differentiation involved in kidney development;negative regulation of canonical Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway;positive regulation of cellular protein catabolic process;beta-catenin destruction complex assembly;beta-catenin destruction complex disassembly
- Cellular component
- cytosol;plasma membrane;nuclear body;intracellular membrane-bounded organelle
- Molecular function
- protein binding;phosphatidylinositol-4,5-bisphosphate binding;beta-catenin binding;beta-catenin destruction complex binding