MAGEE2
Basic information
Region (hg38): X:75782987-75785254
Links
Phenotypes
GenCC
Source:
- male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: XL
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 MAGEE2 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 | 4 | |||||
missense | 23 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 23 | 5 | 2 |
Variants in MAGEE2
This is a list of pathogenic ClinVar variants found in the MAGEE2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-75783503-T-A | not specified | Uncertain significance (Dec 19, 2023) | ||
X-75783503-T-G | not specified | Uncertain significance (Nov 29, 2023) | ||
X-75783601-A-T | not specified | Uncertain significance (May 16, 2024) | ||
X-75783667-T-C | not specified | Uncertain significance (Jul 20, 2022) | ||
X-75783682-T-C | not specified | Uncertain significance (Oct 03, 2023) | ||
X-75783832-A-T | not specified | Uncertain significance (Nov 06, 2023) | ||
X-75783840-T-C | Benign (Dec 31, 2019) | |||
X-75783883-T-A | not specified | Uncertain significance (Mar 21, 2022) | ||
X-75783890-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
X-75784031-T-C | not specified | Uncertain significance (Nov 01, 2022) | ||
X-75784037-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
X-75784065-C-T | not specified | Uncertain significance (May 11, 2022) | ||
X-75784147-C-T | not specified | Uncertain significance (May 16, 2024) | ||
X-75784172-T-C | not specified | Likely benign (Jan 03, 2024) | ||
X-75784184-C-T | not specified | Uncertain significance (Aug 24, 2022) | ||
X-75784332-C-T | Likely benign (Jul 01, 2022) | |||
X-75784341-C-T | Benign (Mar 29, 2018) | |||
X-75784393-C-G | not specified | Uncertain significance (Nov 09, 2023) | ||
X-75784449-G-A | Likely benign (Feb 01, 2023) | |||
X-75784474-C-G | not specified | Uncertain significance (May 08, 2023) | ||
X-75784544-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
X-75784561-A-G | not specified | Likely benign (Jun 07, 2023) | ||
X-75784574-G-A | not specified | Uncertain significance (May 16, 2022) | ||
X-75784616-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
X-75784641-G-C | not specified | Uncertain significance (Apr 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
MAGEE2 | protein_coding | protein_coding | ENST00000373359 | 1 | 2257 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.97e-12 | 0.00894 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -1.74 | 269 | 200 | 1.35 | 0.0000147 | 3459 |
Missense in Polyphen | 123 | 99.278 | 1.2389 | 1815 | ||
Synonymous | -1.25 | 96 | 81.6 | 1.18 | 0.00000632 | 1018 |
Loss of Function | -0.875 | 16 | 12.6 | 1.27 | 0.00000115 | 174 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
Intolerance Scores
- loftool
- 0.857
- rvis_EVS
- -0.2
- rvis_percentile_EVS
- 39.11
Haploinsufficiency Scores
- pHI
- 0.0895
- hipred
- N
- hipred_score
- 0.131
- ghis
- 0.536
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Magee2
- Phenotype