MAGED1

MAGE family member D1, the group of MAGE family

Basic information

Region (hg38): X:51803006-51902354

Links

ENSG00000179222 ∙ NCBI:9500 ∙ OMIM:300224 ∙ HGNC:6813 ∙ Uniprot:Q9Y5V3 ∙ 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 MAGED1 gene.

• Inborn genetic diseases (20 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGED1 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	2	3	6
missense			18	5	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	7	4

Variants in MAGED1

This is a list of pathogenic ClinVar variants found in the MAGED1 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-51894655-A-G		not specified	Likely benign (Dec 03, 2021)
X-51894750-G-A			Benign (Dec 31, 2019)
X-51894787-C-T		not specified	Likely benign (Nov 01, 2022)
X-51895058-G-C		not specified	Uncertain significance (Oct 27, 2022)
X-51895136-C-G		not specified	Uncertain significance (Dec 19, 2022)
X-51895140-G-A		not specified	Uncertain significance (Dec 07, 2021)
X-51895182-G-A		not specified	Uncertain significance (Feb 22, 2023)
X-51895203-C-G		not specified	Uncertain significance (Jan 09, 2023)
X-51895314-G-A		not specified	Likely benign (Sep 26, 2022)
X-51895420-C-A		not specified	Uncertain significance (Jan 22, 2024)
X-51895508-C-T			Uncertain significance (Aug 01, 2017)
X-51895557-T-C		not specified	Uncertain significance (Feb 05, 2024)
X-51895605-G-A		not specified	Uncertain significance (Jul 08, 2022)
X-51895639-A-G		not specified	Uncertain significance (Jan 19, 2024)
X-51895693-C-T		not specified	Uncertain significance (Apr 05, 2023)
X-51895755-C-T		not specified	Uncertain significance (Apr 07, 2022)
X-51896523-G-A		not specified	Uncertain significance (Sep 16, 2021)
X-51896530-C-G		not specified	Uncertain significance (Dec 21, 2023)
X-51896549-G-A			Likely benign (Feb 09, 2018)
X-51896650-G-T		not specified	Uncertain significance (Nov 07, 2022)
X-51896664-G-A		not specified	Uncertain significance (Oct 05, 2023)
X-51896690-A-G			Likely benign (Oct 01, 2022)
X-51896717-G-A			Benign (Aug 16, 2018)
X-51896723-G-T		not specified	Uncertain significance (Jun 28, 2022)
X-51896761-C-T		not specified	Uncertain significance (Aug 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGED1	protein_coding	protein_coding	ENST00000375695	12	99351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00169	125698	4	10	125712	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.33	210	329	0.639	0.0000252	5420
Missense in Polyphen		15	63.709	0.23545		1142
Synonymous	1.34	103	122	0.846	0.00000924	1706
Loss of Function	4.50	2	27.4	0.0729	0.00000198	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000112	0.000112
Ashkenazi Jewish	0.000134	0.0000992
East Asian	0.00	0.00
Finnish	0.0000648	0.0000462
European (Non-Finnish)	0.000100	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000226	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the apoptotic response after nerve growth factor (NGF) binding in neuronal cells. Inhibits cell cycle progression, and facilitates NGFR-mediated apoptosis. May act as a regulator of the function of DLX family members. May enhance ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases. Proposed to act through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. Plays a role in the circadian rhythm regulation. May act as RORA co-regulator, modulating the expression of core clock genes such as ARNTL/BMAL1 and NFIL3, induced, or NR1D1, repressed. {ECO:0000269|PubMed:20864041}.
• Pathway: Neurotrophin signaling pathway - Homo sapiens (human);Signal Transduction;Caspase activation via extrinsic apoptotic signalling pathway;Apoptosis;Programmed Cell Death;NRAGE signals death through JNK;Ligand-independent caspase activation via DCC;Death Receptor Signalling;p75 NTR receptor-mediated signalling;Neurotrophic factor-mediated Trk receptor signaling;p75(NTR)-mediated signaling;Cell death signalling via NRAGE, NRIF and NADE (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.600
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.329
• hipred: Y
• hipred_score: 0.633
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Maged1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; immune system phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;circadian regulation of gene expression;regulation of circadian rhythm;regulation of apoptotic process;positive regulation of MAP kinase activity;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of epithelial cell proliferation;positive regulation of branching involved in ureteric bud morphogenesis;positive regulation of apoptotic signaling pathway
• Cellular component: chromatin;nucleus;cytoplasm;plasma membrane;protein-containing complex
• Molecular function: transcription coactivator activity;protein binding;identical protein binding