MAGEC3

protein-coding

MAGE family member C3, the group of MAGE family

Gene summary

This gene is a member of the MAGEC gene family. The members of this family are not expressed in normal tissues, except for testis, and are expressed in tumors of various histological types. The MAGEC genes are clustered on chromosome Xq26-q27. Two transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_138702.1

Inheritance

—

ClinVar variants

U:140B:12

Top phenotype

MAGEC3-related disorder

gnomAD constraint

pLI —, LoF o/e 1.21

Max pathogenic AF

—

Genomic locus

chrX:141,838,316-141,897,832

External References & Databases

Ensembl (ENSG00000165509)

Transcript & Mutation Effects

hg38 • Region Span ~59.5 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 MAGEC3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 6

MAGEC3-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138702.1. 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			15 clinvar	1 clinvar		16
missense			111 clinvar	9 clinvar	1 clinvar	121
nonsense			8 clinvar			8
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	140	10	2	152

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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_138702.1	RefSeq	NP_619647.1	8	MANE Select
ENST00000298296.1	Ensembl	ENSP00000298296.1	8	MANE Select
NM_177456.2	RefSeq	NP_803251.1	1	Standard
ENST00000409007.1	Ensembl	ENSP00000386566.1	1	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298296
Coding exons: 8
Length: 59517
Individuals with no LoFs: 125704
Homozygous LoFs: 6
Heterozygous LoFs: 16
Defined: 125726
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.949	278	237	1.17	0.0000170	4213
Missense (PolyPhen)		37	32.366	1.1432		649
Synonymous	-1.67	114	93.5	1.22	0.00000714	1249
Loss of Function	-0.826	21	17.3	1.21	0.00000131	294

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.000038	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00012	rare
South Asian	0.00010	0.000065	rare
Other	0.00022	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.887
RVIS EVS: 1.36
RVIS percentile EVS: 94.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0475

Gene Damage Prediction

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