AMN1
Basic information
Region (hg38): 12:31671142-31729121
Links
Phenotypes
GenCC
Source:
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 AMN1 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 | 1 | |||||
missense | 9 | |||||
nonsense | 0 | |||||
start loss | 1 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 1 | |||||
Total | 0 | 0 | 11 | 1 | 0 |
Variants in AMN1
This is a list of pathogenic ClinVar variants found in the AMN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-31689057-T-G | not specified | Uncertain significance (Jan 02, 2024) | ||
12-31689060-G-A | not specified | Uncertain significance (Jun 01, 2023) | ||
12-31689064-G-A | not specified | Uncertain significance (Sep 01, 2021) | ||
12-31689093-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
12-31689097-C-T | not specified | Uncertain significance (May 06, 2024) | ||
12-31689109-T-C | not specified | Uncertain significance (May 23, 2023) | ||
12-31697381-G-T | not specified | Uncertain significance (Mar 20, 2024) | ||
12-31697817-T-G | not specified | Uncertain significance (Jan 04, 2024) | ||
12-31697841-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
12-31697938-T-G | Likely benign (Mar 01, 2023) | |||
12-31697949-C-A | not specified | Uncertain significance (Dec 11, 2023) | ||
12-31701943-A-T | not specified | Uncertain significance (Mar 24, 2023) | ||
12-31728977-A-C | not specified | Uncertain significance (Jan 11, 2023) | ||
12-31729002-G-A | not specified | Uncertain significance (Nov 17, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AMN1 | protein_coding | protein_coding | ENST00000281471 | 7 | 58038 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.325 | 0.672 | 124602 | 1 | 8 | 124611 | 0.0000361 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.25 | 92 | 133 | 0.693 | 0.00000674 | 1653 |
Missense in Polyphen | 30 | 41.335 | 0.72578 | 555 | ||
Synonymous | 0.769 | 43 | 49.9 | 0.862 | 0.00000276 | 505 |
Loss of Function | 2.54 | 3 | 12.8 | 0.234 | 6.17e-7 | 174 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000145 | 0.000145 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000366 | 0.0000354 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000347 | 0.0000327 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.706
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- N
- hipred_score
- 0.394
- ghis
- 0.617
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.417
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amn1
- Phenotype
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
- Cellular component
- SCF ubiquitin ligase complex
- Molecular function
- ubiquitin-protein transferase activity