MAGEC2

MAGE family member C2, the group of MAGE family

Basic information

Region (hg38): X:142202342-142205290

Previous symbols: [ "MAGEE1" ]

Links

ENSG00000046774 ∙ NCBI:51438 ∙ OMIM:300468 ∙ HGNC:13574 ∙ Uniprot:Q9UBF1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAGEC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEC2 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				5	1	6
missense			16	1	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	6	2

Variants in MAGEC2

This is a list of pathogenic ClinVar variants found in the MAGEC2 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-142202918-A-G		not specified	Uncertain significance (Nov 16, 2021)
X-142202938-G-A			Likely benign (Jun 01, 2022)
X-142203009-T-C		not specified	Uncertain significance (Nov 21, 2022)
X-142203051-T-C		not specified	Uncertain significance (May 30, 2023)
X-142203080-G-A		not specified	Uncertain significance (Jun 27, 2023)
X-142203119-G-A		not specified	Uncertain significance (May 16, 2023)
X-142203164-G-C			Benign (Mar 02, 2018)
X-142203177-T-C		not specified	Uncertain significance (Mar 07, 2023)
X-142203247-C-G		not specified	Uncertain significance (Apr 23, 2024)
X-142203250-C-T			Likely benign (Mar 01, 2023)
X-142203342-C-T		not specified	Uncertain significance (Oct 20, 2023)
X-142203402-C-T		not specified	Uncertain significance (Apr 07, 2022)
X-142203403-A-G			Benign (Nov 29, 2017)
X-142203432-G-A		not specified	Uncertain significance (Sep 14, 2023)
X-142203520-G-A			Likely benign (Sep 01, 2022)
X-142203540-C-G		not specified	Likely benign (Oct 25, 2023)
X-142203542-A-G		not specified	Uncertain significance (Jan 30, 2024)
X-142203591-T-G		not specified	Uncertain significance (Mar 25, 2022)
X-142203631-C-T			Likely benign (May 01, 2022)
X-142203707-C-A		not specified	Uncertain significance (Dec 20, 2023)
X-142203710-T-C		not specified	Uncertain significance (Jan 03, 2022)
X-142203716-G-A		not specified	Uncertain significance (Nov 04, 2023)
X-142203925-C-T			Likely benign (Sep 01, 2022)
X-142203938-G-A		not specified	Uncertain significance (Sep 27, 2021)
X-142203969-C-T		not specified	Uncertain significance (Oct 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEC2	protein_coding	protein_coding	ENST00000247452	1	2946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.653	164	142	1.15	0.0000105	2451
Missense in Polyphen		34	34.549	0.98411		724
Synonymous	-1.99	80	60.4	1.33	0.00000488	755
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed to enhance ubiquitin ligase activity of RING- type zinc finger-containing E3 ubiquitin-protein ligases. In vitro enhances ubiquitin ligase activity of TRIM28 and stimulates p53/TP53 ubiquitination in presence of Ubl-conjugating enzyme UBE2H leading to p53/TP53 degradation. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzymes (E2) at the E3:substrate complex. {ECO:0000269|PubMed:20864041}.

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.0303
• hipred: N
• hipred_score: 0.246
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00149

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Magee1

Gene ontology

• Biological process: cellular protein catabolic process;positive regulation of ubiquitin-protein transferase activity
• Cellular component: nucleus;nucleolus;cytoplasm;cytosol
• Molecular function: protein binding;ubiquitin protein ligase binding