MAGEE2

MAGE family member E2, the group of MAGE family

Basic information

Region (hg38): X:75782987-75785254

Links

ENSG00000186675 ∙ NCBI:139599 ∙ OMIM:300760 ∙ HGNC:24935 ∙ Uniprot:Q8TD90 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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	2	4
missense			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	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-75783569-A-G		not specified	Uncertain significance (Dec 22, 2024)
X-75783599-C-A		not specified	Uncertain significance (Jan 24, 2025)
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-75783710-G-A		not specified	Uncertain significance (Dec 03, 2024)
X-75783769-C-T		not specified	Uncertain significance (Feb 12, 2025)
X-75783809-C-A		not specified	Uncertain significance (Feb 14, 2025)
X-75783832-A-T		not specified	Uncertain significance (Nov 06, 2023)
X-75783840-T-C			Benign (Dec 31, 2019)
X-75783863-C-T		not specified	Uncertain significance (Jan 15, 2025)
X-75783883-T-A		not specified	Uncertain significance (Mar 21, 2022)
X-75783890-C-T		not specified	Uncertain significance (Jan 22, 2025)
X-75783899-C-G		not specified	Uncertain significance (Aug 12, 2024)
X-75783959-C-T		not specified	Uncertain significance (Sep 24, 2024)
X-75784031-T-C		not specified	Uncertain significance (Nov 27, 2024)
X-75784037-C-T		not specified	Uncertain significance (Jan 30, 2024)
X-75784058-T-C		not specified	Uncertain significance (Sep 10, 2024)
X-75784065-C-T		not specified	Uncertain significance (Sep 02, 2024)
X-75784104-A-T		not specified	Uncertain significance (Feb 14, 2025)
X-75784147-C-T		not specified	Uncertain significance (May 16, 2024)
X-75784158-G-T		not specified	Uncertain significance (Jan 21, 2025)
X-75784172-T-C		not specified	Likely benign (Jan 03, 2024)

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Magee2