MAGEB2

MAGE family member B2, the group of MAGE family

Basic information

Region (hg38): X:30215563-30220089

Links

ENSG00000099399 ∙ NCBI:4113 ∙ OMIM:300098 ∙ HGNC:6809 ∙ Uniprot:O15479 ∙ 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 MAGEB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEB2 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				3		3
missense			15	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	6	1

Variants in MAGEB2

This is a list of pathogenic ClinVar variants found in the MAGEB2 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-30218623-C-T		not specified	Conflicting classifications of pathogenicity (Jan 01, 2023)
X-30218647-C-T		not specified	Uncertain significance (Jul 20, 2021)
X-30218657-A-G		not specified	Uncertain significance (Aug 08, 2022)
X-30218661-TC-T		Autism	Uncertain significance (-)
X-30218696-C-A		not specified	Uncertain significance (May 08, 2023)
X-30218698-T-A		not specified	Likely benign (Jan 24, 2023)
X-30218704-T-C		not specified	Uncertain significance (Jan 23, 2023)
X-30218798-C-A		not specified	Uncertain significance (May 02, 2024)
X-30218853-G-T		not specified	Uncertain significance (Jun 05, 2023)
X-30218887-A-G			Benign (Mar 30, 2018)
X-30218940-G-C		not specified	Uncertain significance (Jan 10, 2023)
X-30218954-A-G		not specified	Uncertain significance (Nov 19, 2022)
X-30218973-C-T			Likely benign (Jul 01, 2022)
X-30219012-G-C		not specified	Uncertain significance (Mar 18, 2024)
X-30219110-C-G		not specified	Likely benign (Sep 17, 2021)
X-30219111-T-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
X-30219169-G-C		not specified	Uncertain significance (Jan 03, 2024)
X-30219183-A-G			Likely benign (Mar 01, 2023)
X-30219188-T-C		not specified	Uncertain significance (Oct 02, 2023)
X-30219196-C-A		not specified	Uncertain significance (Dec 03, 2021)
X-30219227-A-G		not specified	Uncertain significance (May 17, 2023)
X-30219276-C-A			Likely benign (Aug 01, 2022)
X-30219295-T-C			Likely benign (Jan 01, 2023)
X-30219350-A-C		not specified	Uncertain significance (Jun 24, 2022)
X-30219438-G-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEB2	protein_coding	protein_coding	ENST00000378988	1	4530

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	-1.30	160	120	1.34	0.00000927	2049
Missense in Polyphen		51	34.91	1.4609		602
Synonymous	0.430	45	48.8	0.922	0.00000385	651
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: May enhance ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. {ECO:0000269|PubMed:20864041}.

Recessive Scores

• pRec: 0.0871

Intolerance Scores

• loftool: 0.645
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00132

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mageb4

Gene ontology

• Molecular function: protein binding