MAGEB16

protein-coding

MAGE family member B16, the group of MAGE family

Gene summary

Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001370158.1

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:35,798,342-35,803,772

External References & Databases

Ensembl (ENSG00000189023)

Transcript & Mutation Effects

hg38 • Region Span ~5.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MAGEB16 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001370158.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			37 clinvar		1 clinvar	38
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	38	1	1	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001370158.1	RefSeq	NP_001357087.1	1	MANE Select
ENST00000399988.6	Ensembl	ENSP00000382870.1	1	MANE Select
NM_001099921.2	RefSeq	NP_001093391.1	1	Standard
NM_001370159.1	RefSeq	NP_001357088.1	1	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399989
Coding exons: 1
Length: 5394
Individuals with no LoFs: 123500
Homozygous LoFs: 15
Heterozygous LoFs: 22
Defined: 123537
p: 0.000150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.577	94	111	0.846	0.00000750	2124
Missense (PolyPhen)		15	28.548	0.52543		602
Synonymous	-0.149	46	44.7	1.03	0.00000313	642
Loss of Function	0.830	0	0.802	0.00	4.88e-8	25

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0027	0.0021	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.746
RVIS EVS: 1.37
RVIS percentile EVS: 94.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0110

Gene Damage Prediction

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