MAGEC1

protein-coding

MAGE family member C1, the group of MAGE family

Gene summary

This gene is a member of the melanoma antigen gene (MAGE) family. The proteins of this family are tumor-specific antigens that can be recognized by autologous cytolytic T lymphocytes. This protein contains a large number of unique short repetitive sequences in front of the MAGE-homologous sequence, and therefore is about 800 aa longer than the other MAGE proteins. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005462.5

Inheritance

—

ClinVar variants

U:207B:54

Top phenotype

Autism

gnomAD constraint

pLI —, LoF o/e 1.35

Max pathogenic AF

—

Genomic locus

chrX:141,903,894-141,909,374

External References & Databases

Ensembl (ENSG00000155495)

Transcript & Mutation Effects

hg38 • Region Span ~5.5 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 MAGEC1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 217

not providedTotal: 50

AutismTotal: 1

MAGEC1-related conditionTotal: 1

Decreased total neutrophil countTotal: 1

Decreased total lymphocyte countTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005462.5. 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			4 clinvar	12 clinvar		16
missense			200 clinvar	36 clinvar	2 clinvar	238
nonsense			1 clinvar			1
start loss				1 clinvar		1
frameshift			2 clinvar	3 clinvar		5
splice donor/acceptor (+/-2bp)						0
Total	0	0	207	52	2	261

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005462.5	RefSeq	NP_005453.2	2	MANE Select
ENST00000285879.5	Ensembl	ENSP00000285879.4	2	MANE Select
ENST00000406005.2	Ensembl	ENSP00000385500.2	1	Standard
ENST00001125965.1	Ensembl	ENSP00000795770.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000285879
Coding exons: 2
Length: 5495
Individuals with no LoFs: 117661
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 117662
p: 0.00000425

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-5.17	665	381	1.75	0.0000271	7415
Missense (PolyPhen)		9	9.775	0.92071		120
Synonymous	-4.50	222	152	1.46	0.0000114	2306
Loss of Function	-0.277	1	0.743	1.35	4.70e-8	12

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000013	0.0000093	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.981
RVIS EVS: 6.42
RVIS percentile EVS: 99.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0486

Gene Damage Prediction

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