AMD1
Basic information
Region (hg38): 6:110874770-110898879
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 AMD1 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 | 6 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 6 | 0 | 0 |
Variants in AMD1
This is a list of pathogenic ClinVar variants found in the AMD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-110887569-A-C | not specified | Uncertain significance (Dec 20, 2022) | ||
6-110888910-C-T | not specified | Uncertain significance (Jun 26, 2024) | ||
6-110888913-C-A | not specified | Uncertain significance (Jul 22, 2022) | ||
6-110888948-C-A | not specified | Uncertain significance (May 05, 2023) | ||
6-110890330-T-C | not specified | Uncertain significance (Nov 15, 2023) | ||
6-110892331-G-A | not specified | Uncertain significance (Jul 30, 2024) | ||
6-110892340-G-C | not specified | Uncertain significance (Oct 07, 2024) | ||
6-110892783-A-G | not specified | Uncertain significance (Sep 11, 2024) | ||
6-110892914-C-T | not specified | Uncertain significance (Jul 20, 2022) | ||
6-110893006-A-G | not specified | Uncertain significance (Apr 26, 2024) | ||
6-110893531-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
6-110893597-A-C | not specified | Uncertain significance (Oct 16, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AMD1 | protein_coding | protein_coding | ENST00000368885 | 9 | 20944 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.982 | 0.0177 | 125733 | 0 | 14 | 125747 | 0.0000557 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.24 | 100 | 186 | 0.537 | 0.00000955 | 2241 |
Missense in Polyphen | 12 | 49.598 | 0.24194 | 711 | ||
Synonymous | 0.537 | 55 | 60.3 | 0.912 | 0.00000285 | 595 |
Loss of Function | 3.56 | 1 | 16.7 | 0.0599 | 7.04e-7 | 216 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000170 | 0.000166 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000279 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000221 | 0.000196 |
Other | 0.000183 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for biosynthesis of the polyamines spermidine and spermine. Promotes maintenance and self-renewal of embryonic stem cells, by maintaining spermine levels. {ECO:0000250|UniProtKB:P0DMN7}.;
- Pathway
- Arginine and proline metabolism - Homo sapiens (human);Cysteine and methionine metabolism - Homo sapiens (human);S-Adenosylhomocysteine (SAH) Hydrolase Deficiency;Methionine Metabolism;Methionine Adenosyltransferase Deficiency;Glycine N-methyltransferase Deficiency;Hypermethioninemia;Methylenetetrahydrofolate Reductase Deficiency (MTHFRD);Homocystinuria-megaloblastic anemia due to defect in cobalamin metabolism, cblG complementation type;Spermidine and Spermine Biosynthesis;Cystathionine Beta-Synthase Deficiency;Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Metabolism;Arginine Proline metabolism;spermidine biosynthesis;methionine salvage cycle III;spermine biosynthesis
(Consensus)
Recessive Scores
- pRec
- 0.290
Intolerance Scores
- loftool
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.766
- hipred
- Y
- hipred_score
- 0.626
- ghis
- 0.597
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.897
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Amd1
- 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);
Gene ontology
- Biological process
- S-adenosylmethioninamine biosynthetic process;polyamine metabolic process;spermine biosynthetic process;spermidine biosynthetic process;S-adenosylmethionine metabolic process
- Cellular component
- cytosol
- Molecular function
- adenosylmethionine decarboxylase activity;putrescine binding