MAGEF1

MAGE family member F1, the group of MAGE family

Basic information

Region (hg38): 3:184710364-184712064

Links

ENSG00000177383 ∙ NCBI:64110 ∙ OMIM:609267 ∙ HGNC:29639 ∙ Uniprot:Q9HAY2 ∙ 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 MAGEF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEF1 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						0
missense			14			14
nonsense						0
start loss						0
frameshift					1	1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	2

Variants in MAGEF1

This is a list of pathogenic ClinVar variants found in the MAGEF1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-184710982-C-G		not specified	Uncertain significance (Apr 27, 2023)
3-184711068-T-A		not specified	Uncertain significance (Jan 23, 2024)
3-184711098-C-T		not specified	Uncertain significance (Dec 15, 2022)
3-184711103-G-A		not specified	Uncertain significance (Jul 20, 2022)
3-184711173-C-A		not specified	Uncertain significance (May 24, 2023)
3-184711238-C-A		not specified	Uncertain significance (Oct 14, 2023)
3-184711258-C-A		not specified	Uncertain significance (Dec 01, 2022)
3-184711299-C-T		not specified	Uncertain significance (Jun 17, 2024)
3-184711326-T-C		not specified	Uncertain significance (Jan 23, 2024)
3-184711331-C-G		not specified	Uncertain significance (Jan 11, 2023)
3-184711332-C-T		not specified	Uncertain significance (Apr 23, 2024)
3-184711345-A-ATCCTCC		not specified	Benign (Mar 29, 2016)
3-184711401-G-A		not specified	Uncertain significance (Mar 25, 2024)
3-184711428-C-G		not specified	Uncertain significance (Jun 06, 2022)
3-184711494-A-C		not specified	Uncertain significance (Sep 22, 2023)
3-184711607-G-A		not specified	Uncertain significance (Nov 17, 2022)
3-184711613-C-G		not specified	Uncertain significance (May 29, 2024)
3-184711634-G-A		not specified	Uncertain significance (May 08, 2023)
3-184711720-C-G		not specified	Uncertain significance (Feb 05, 2024)
3-184711769-T-TC			Benign (Dec 19, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEF1	protein_coding	protein_coding	ENST00000317897	1	1681

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00301	0.605	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0429	173	171	1.01	0.00000790	1975
Missense in Polyphen		50	45.14	1.1077		526
Synonymous	1.79	54	73.5	0.735	0.00000352	628
Loss of Function	0.417	4	5.01	0.799	2.09e-7	80

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin ligases. Proposed to act through recruitment and/or stabilization of the E2 ubiquitin-conjugating enzyme at the E3:substrate complex. MAGEF1-NSMCE1 ubiquitin ligase complex promotes proteasomal degradation of MMS19, a key component of the cytosolic iron-sulfur protein assembly (CIA) machinery. Down-regulation of MMS19 impairs the activity of several DNA repair and metabolism enzymes such as ERCC2/XPD, FANCJ, RTEL1 and POLD1 that require iron-sulfur clusters as cofactors. May negatively regulate genome integrity by inhibiting homologous recombination-mediated double-strand break DNA repair (PubMed:29225034). {ECO:0000269|PubMed:20864041, ECO:0000269|PubMed:29225034}.

Recessive Scores

• pRec: 0.0958

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.47

Haploinsufficiency Scores

• pHI: 0.0575
• hipred: N
• hipred_score: 0.180
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0923

Gene Damage Prediction

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

Gene ontology

• Biological process: protein ubiquitination;protein maturation by iron-sulfur cluster transfer;negative regulation of double-strand break repair via homologous recombination;positive regulation of ubiquitin-dependent protein catabolic process
• Molecular function: protein binding