AMER3
protein-codingAPC membrane recruitment protein 3, the group of APC membrane recruitment proteins
Gene summary
Predicted to enable beta-catenin binding activity and phosphatidylinositol-4,5-bisphosphate binding activity. Predicted to be involved in regulation of canonical Wnt signaling pathway. Located in nuclear body. [provided by Alliance of Genome Resources, Jun 2026]
- FAM123C
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to AMER3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_152698.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 141 | 16 | 157 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 141 | 17 | 0 | 159 |
Highest pathogenic variant AF is 0.00002426212
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_689911.2 | 1 | MANE Select | |
| Ensembl | ENSP00000314914.4 | 1 | MANE Select | |
| RefSeq | NP_001098663.1 | 1 | Standard | |
| RefSeq | NP_001098664.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- Wnt signaling pathway
- regulation of canonical Wnt signaling pathway
Molecular Function
- protein binding
- phosphatidylinositol-4,5-bisphosphate binding
- beta-catenin binding
Cellular Component
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000423981
- Coding exons
- 1
- Length
- 12700
- Individuals with no LoFs
- 125724
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 8
- Defined
- 125732
- p
- 0.0000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.671 | 561 | 518 | 1.08 | 0.0000315 | 5473 |
| Missense (PolyPhen) | 129 | 149.25 | 0.86431 | 1689 | ||
| Synonymous | -1.74 | 265 | 231 | 1.15 | 0.0000153 | 1894 |
| Loss of Function | 2.62 | 2 | 11.7 | 0.171 | 6.59e-7 | 126 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000074 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.0000089 | 0.0000088 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
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 (By similarity). {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- -1.08
- RVIS percentile EVS
- 7.24
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |