MAGEE2

MAGE family member E2, the group of MAGE family

Basic information

Region (hg38): X:75782987-75785254

Links

ENSG00000186675NCBI:139599OMIM:300760HGNC:24935Uniprot:Q8TD90AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • 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 ClinVar and linked to the MAGEE2 gene.

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
2
clinvar
2
clinvar
4
missense
23
clinvar
3
clinvar
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)3122206
X-75783503-T-G not specified Uncertain significance (Nov 29, 2023)3122205
X-75783601-A-T not specified Uncertain significance (May 16, 2024)3292672
X-75783667-T-C not specified Uncertain significance (Jul 20, 2022)3122204
X-75783682-T-C not specified Uncertain significance (Oct 03, 2023)3122203
X-75783832-A-T not specified Uncertain significance (Nov 06, 2023)3122201
X-75783840-T-C Benign (Dec 31, 2019)782729
X-75783883-T-A not specified Uncertain significance (Mar 21, 2022)2279260
X-75783890-C-T not specified Uncertain significance (Dec 02, 2022)3122200
X-75784031-T-C not specified Uncertain significance (Nov 01, 2022)2380582
X-75784037-C-T not specified Uncertain significance (Jan 30, 2024)3122198
X-75784065-C-T not specified Uncertain significance (May 11, 2022)2305753
X-75784147-C-T not specified Uncertain significance (May 16, 2024)3292675
X-75784172-T-C not specified Likely benign (Jan 03, 2024)3122209
X-75784184-C-T not specified Uncertain significance (Aug 24, 2022)2306120
X-75784332-C-T Likely benign (Jul 01, 2022)2660948
X-75784341-C-T Benign (Mar 29, 2018)771227
X-75784393-C-G not specified Uncertain significance (Nov 09, 2023)3122208
X-75784449-G-A Likely benign (Feb 01, 2023)2660949
X-75784474-C-G not specified Uncertain significance (May 08, 2023)2545090
X-75784544-C-T not specified Uncertain significance (Sep 17, 2021)2281060
X-75784561-A-G not specified Likely benign (Jun 07, 2023)2552313
X-75784574-G-A not specified Uncertain significance (May 16, 2022)2289772
X-75784616-C-T not specified Uncertain significance (Dec 06, 2022)2366828
X-75784641-G-C not specified Uncertain significance (Apr 01, 2024)3292674

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MAGEE2protein_codingprotein_codingENST00000373359 12257
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.97e-120.0089400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.742692001.350.00001473459
Missense in Polyphen12399.2781.23891815
Synonymous-1.259681.61.180.000006321018
Loss of Function-0.8751612.61.270.00000115174

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Magee2
Phenotype