AMFR
autocrine motility factor receptor, the group of Ring finger proteins
Basic information
Region (hg38): 16:56361451-56425545
Links
Phenotypes
GenCC
Source:
- spastic paraplegia 89, autosomal recessive (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spastic paraplegia 89, autosomal recessive | AR | 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 | Neurologic | 37119330 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (19 variants)
- Marfanoid habitus and intellectual disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMFR 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 | 18 | 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 | 18 | 2 | 0 |
Variants in AMFR
This is a list of pathogenic ClinVar variants found in the AMFR region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AMFR | protein_coding | protein_coding | ENST00000290649 | 14 | 64087 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000584 | 1.00 | 125711 | 0 | 37 | 125748 | 0.000147 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.87 | 267 | 368 | 0.726 | 0.0000229 | 4205 |
| Missense in Polyphen | 50 | 87.182 | 0.57351 | 881 | ||
| Synonymous | 1.30 | 118 | 137 | 0.859 | 0.00000894 | 1284 |
| Loss of Function | 3.20 | 13 | 32.8 | 0.396 | 0.00000183 | 354 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000152 | 0.000152 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.000832 | 0.000832 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000371 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase that mediates the polyubiquitination of a number of proteins such as CD3D, CYP3A4, CFTR and APOB for proteasomal degradation. Component of a VCP/p97- AMFR/gp78 complex that participates in the final step of endoplasmic reticulum-associated degradation (ERAD). The VCP/p97- AMFR/gp78 complex is involved in the sterol-accelerated ERAD degradation of HMGCR through binding to the HMGCR-INSIG complex at the ER membrane and initiating ubiquitination of HMGCR. The ubiquitinated HMGCR is then released from the ER by the complex into the cytosol for subsequent destruction. Also regulates ERAD through the ubiquitination of UBL4A a component of the BAG6/BAT3 complex. Also acts as a scaffold protein to assemble a complex that couples ubiquitination, retranslocation and deglycosylation. Mediates tumor invasion and metastasis as a receptor for the GPI/autocrine motility factor. {ECO:0000269|PubMed:10456327, ECO:0000269|PubMed:11724934, ECO:0000269|PubMed:16168377, ECO:0000269|PubMed:19103148, ECO:0000269|PubMed:24424410}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle
(Consensus)
Recessive Scores
- pRec
- 0.172
Intolerance Scores
- loftool
- 0.602
- rvis_EVS
- -1.09
- rvis_percentile_EVS
- 7.05
Haploinsufficiency Scores
- pHI
- 0.317
- hipred
- Y
- hipred_score
- 0.652
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.876
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amfr
- Phenotype
- liver/biliary system phenotype; neoplasm; immune system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- protein polyubiquitination;protein folding;ubiquitin-dependent protein catabolic process;signal transduction;aging;learning or memory;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;positive regulation of protein binding;protein complex oligomerization;protein autoubiquitination;protein K48-linked ubiquitination;endoplasmic reticulum mannose trimming
- Cellular component
- nucleus;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;membrane;integral component of membrane;integral component of endoplasmic reticulum membrane;dendrite;growth cone;protein-containing complex;Derlin-1 retrotranslocation complex;neuronal cell body;endoplasmic reticulum quality control compartment;perinuclear region of cytoplasm
- Molecular function
- ubiquitin-protein transferase activity;protein binding;protein binding, bridging;ubiquitin-ubiquitin ligase activity;signaling receptor activity;identical protein binding;metal ion binding;chaperone binding;ubiquitin protein ligase activity;BAT3 complex binding;ubiquitin-specific protease binding