AMTN
Basic information
Region (hg38): 4:70518569-70532743
Links
Phenotypes
GenCC
Source:
- amelogenesis imperfecta, type 3A (Supportive), mode of inheritance: AD
- amelogenesis imperfecta type 3B (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Amelogenesis imperfecta, type IIIB | AD | 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 | Dental | 27412008 |
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 AMTN 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 | 14 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 8 | 3 | 4 |
Variants in AMTN
This is a list of pathogenic ClinVar variants found in the AMTN 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 |
|---|---|---|---|---|---|
| AMTN | protein_coding | protein_coding | ENST00000339336 | 8 | 14203 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.13e-11 | 0.0215 | 125714 | 0 | 16 | 125730 | 0.0000636 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.380 | 99 | 110 | 0.898 | 0.00000539 | 1301 |
| Missense in Polyphen | 20 | 20.657 | 0.96818 | 260 | ||
| Synonymous | -0.489 | 48 | 43.9 | 1.09 | 0.00000226 | 453 |
| Loss of Function | -0.704 | 14 | 11.4 | 1.22 | 4.85e-7 | 138 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000121 | 0.000121 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000797 | 0.0000791 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Is a promoter of calcium phosphate mineralization, playing a critical role in the formation of the compact, mineralized, aprismatic enamel surface layer during the maturation stage of amelogenesis. {ECO:0000269|PubMed:25407797}.;
- Disease
- DISEASE: Amelogenesis imperfecta 3B (AI3B) [MIM:617607]: An autosomal dominant form of amelogenesis imperfecta, a defect of enamel formation. AI3B is characterized by hypomineralized enamel that has reduced tickness and exhibits structural defects. {ECO:0000269|PubMed:27412008}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
(Consensus)
Recessive Scores
- pRec
- 0.0547
Intolerance Scores
- loftool
- 0.763
- rvis_EVS
- 1.3
- rvis_percentile_EVS
- 93.95
Haploinsufficiency Scores
- pHI
- 0.0448
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0517
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amtn
- Phenotype
- skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype;
Gene ontology
- Biological process
- cell adhesion;biomineral tissue development;odontogenesis of dentin-containing tooth;post-translational protein modification;cellular protein metabolic process;positive regulation of biomineral tissue development;positive regulation of enamel mineralization
- Cellular component
- basement membrane;endoplasmic reticulum lumen;cell-cell junction;extracellular matrix
- Molecular function
- molecular_function;protein binding