MAGEC3

MAGE family member C3, the group of MAGE family

Basic information

Region (hg38): X:141838316-141897832

Links

ENSG00000165509 ∙ NCBI:139081 ∙ OMIM:300469 ∙ HGNC:23798 ∙ Uniprot:Q8TD91 ∙ 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 MAGEC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEC3 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		1
missense			32	5	1	38
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	32	6	2

Variants in MAGEC3

This is a list of pathogenic ClinVar variants found in the MAGEC3 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-141838356-G-C		not specified	Uncertain significance (Oct 01, 2024)
X-141838379-G-A		not specified	Uncertain significance (May 27, 2022)
X-141865468-T-C			Likely benign (Mar 01, 2023)
X-141865475-G-A		not specified	Likely benign (Dec 21, 2022)
X-141865475-G-T		not specified	Uncertain significance (Jan 31, 2024)
X-141865490-A-T		not specified	Uncertain significance (Sep 26, 2022)
X-141865547-G-A		not specified	Uncertain significance (Apr 18, 2023)
X-141865568-G-T		not specified	Uncertain significance (Oct 19, 2024)
X-141879188-T-C		not specified	Likely benign (Dec 20, 2021)
X-141879239-C-T		not specified	Likely benign (Jul 06, 2021)
X-141879310-A-C		not specified	Uncertain significance (Oct 14, 2023)
X-141879364-A-C		not specified	Uncertain significance (Apr 07, 2022)
X-141879368-GCTACACCCTTTCCCTTC-G			Benign (Dec 31, 2019)
X-141879388-G-A		not specified	Uncertain significance (Nov 08, 2024)
X-141879391-G-A			Likely benign (Feb 01, 2023)
X-141879394-A-G		not specified	Uncertain significance (Dec 08, 2021)
X-141879413-G-C		not specified	Uncertain significance (Feb 16, 2023)
X-141879425-C-G		not specified	Uncertain significance (May 09, 2024)
X-141881416-G-C		not specified	Uncertain significance (Apr 09, 2024)
X-141881494-G-A		not specified	Uncertain significance (Aug 02, 2021)
X-141881537-C-G		not specified	Likely benign (Dec 14, 2021)
X-141881543-C-T		not specified	Uncertain significance (Jul 31, 2024)
X-141881554-C-G		not specified	Uncertain significance (Apr 04, 2024)
X-141881570-A-G			Benign (Dec 31, 2019)
X-141881576-G-C		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEC3	protein_coding	protein_coding	ENST00000298296	8	59517

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.66e-16	0.00233	125704	6	16	125726	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.949	278	237	1.17	0.0000170	4213
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000114	0.0000993
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000173	0.000123
Middle Eastern	0.000217	0.000163
South Asian	0.000105	0.0000653
Other	0.000223	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.887
• rvis_EVS: 1.36
• rvis_percentile_EVS: 94.44

Haploinsufficiency Scores

• pHI: 0.0579
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0475

Gene Damage Prediction

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