MAGEB4

MAGE family member B4, the group of MAGE family

Basic information

Region (hg38): X:30242000-30244187

Links

ENSG00000120289 ∙ NCBI:4115 ∙ OMIM:300153 ∙ HGNC:6811 ∙ Uniprot:O15481 ∙ 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 MAGEB4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEB4 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				1	2	3
missense			10	1	3	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	5

Variants in MAGEB4

This is a list of pathogenic ClinVar variants found in the MAGEB4 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-30242163-C-T		not specified	Uncertain significance (Nov 09, 2021)
X-30242184-C-G		not specified	Uncertain significance (Dec 21, 2022)
X-30242191-G-A			Benign (Dec 31, 2019)
X-30242210-C-T			Benign (Sep 19, 2018)
X-30242218-G-A		not specified	Uncertain significance (Jun 05, 2024)
X-30242338-C-T		not specified	Uncertain significance (Jun 16, 2024)
X-30242341-C-T		not specified	Uncertain significance (Oct 29, 2021)
X-30242371-G-T		not specified	Uncertain significance (Nov 22, 2021)
X-30242416-C-T		not specified	Uncertain significance (Jun 18, 2024)
X-30242451-A-G		not specified	Uncertain significance (Dec 22, 2023)
X-30242489-G-A			Benign (Dec 31, 2019)
X-30242833-A-G		not specified	Uncertain significance (Jul 09, 2021)
X-30242840-C-T			Likely benign (Jul 31, 2018)
X-30242844-A-G		not specified	Uncertain significance (Apr 01, 2024)
X-30242860-G-A		not specified	Uncertain significance (Nov 29, 2023)
X-30242934-C-A			Benign (Dec 31, 2019)
X-30242968-C-A		not specified	Uncertain significance (Jan 04, 2024)
X-30243094-G-C			Likely benign (Aug 01, 2022)
X-30243118-C-T		not specified	Uncertain significance (Oct 13, 2023)
X-30243124-T-C			Benign (Dec 31, 2019)
X-30243154-G-A		not specified	Uncertain significance (Dec 17, 2023)
X-30243176-A-T			Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEB4	protein_coding	protein_coding	ENST00000378982	1	2237

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	0.591	114	133	0.856	0.0000105	2254
Missense in Polyphen		15	32.337	0.46387		640
Synonymous	-1.20	60	49.3	1.22	0.00000357	707
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

Recessive Scores

• pRec: 0.0845

Intolerance Scores

• loftool: 0.119
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.0276
• hipred: N
• hipred_score: 0.112
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Gene ontology

• Cellular component: cytoplasm
• Molecular function: protein binding