MAGEL2

MAGE family member L2, the group of MAGE family

Basic information

Region (hg38): 15:23643549-23647867

Previous symbols: [ "NDNL1" ]

Links

ENSG00000254585 ∙ NCBI:54551 ∙ OMIM:605283 ∙ HGNC:6814 ∙ Uniprot:Q9UJ55 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Schaaf-Yang syndrome (Definitive), mode of inheritance: Autosomal dominant inheritance with maternal imprinting HP:0012275
• Schaaf-Yang syndrome (Strong), mode of inheritance: AD
• Schaaf-Yang syndrome (Definitive), mode of inheritance: AD
• Schaaf-Yang syndrome (Definitive), mode of inheritance: AD
• Schaaf-Yang syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Schaaf-Yang syndrome (Prader-Willi-like syndrome)	AD	Endocrine	The condition has been described as including neonatal hyperinsulinemia hypoglycemia, and awareness may allow prompt management	Craniofacial; Endocrine; Genitourinary; Musculoskeletal; Neurologic	24076603; 25473036; 26365340; 27195816; 28281571

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAGEL2 gene.

• not provided (20 variants)
• Schaaf-Yang syndrome (16 variants)
• Inborn genetic diseases (5 variants)
• Prader-Willi syndrome (2 variants)
• Generalized hypotonia;Ventriculomegaly;Multiple joint contractures;Ambiguous genitalia (1 variants)
• Schaaf-Yang syndrome;Prader-Willi-like syndrome (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental disorder (1 variants)
• Neurodevelopmental delay (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGEL2 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			33	163	11	207
missense	1		450	43	7	501
nonsense	14	11	3			28
start loss		1				1
frameshift	22	18	3			43
inframe indel			41	6		47
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		2	3
Total	37	30	531	212	20

Variants in MAGEL2

This is a list of pathogenic ClinVar variants found in the MAGEL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-23643744-A-T			Benign (Jul 09, 2018)
15-23643886-G-T			Benign (Jul 09, 2018)
15-23643995-A-T			Uncertain significance (Apr 01, 2023)
15-23643997-C-T		MAGEL2-related disorder	Conflicting classifications of pathogenicity (Aug 28, 2023)
15-23643998-G-A			Uncertain significance (Jun 15, 2023)
15-23643998-G-C			Uncertain significance (Jul 26, 2023)
15-23644003-G-A			Uncertain significance (Jan 03, 2023)
15-23644004-G-C		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
15-23644015-G-A			Uncertain significance (Dec 05, 2022)
15-23644016-T-C		Schaaf-Yang syndrome	Uncertain significance (Aug 01, 2022)
15-23644020-G-T			Uncertain significance (May 08, 2023)
15-23644022-C-T			Benign/Likely benign (Nov 24, 2023)
15-23644023-G-T		Schaaf-Yang syndrome	Uncertain significance (Feb 14, 2023)
15-23644026-G-T			Likely benign (Jun 04, 2022)
15-23644030-C-T		MAGEL2-related disorder	Uncertain significance (May 21, 2024)
15-23644037-C-T		MAGEL2-related disorder	Uncertain significance (Dec 11, 2023)
15-23644038-G-C			Likely benign (Apr 18, 2022)
15-23644039-G-T		MAGEL2-related disorder	Uncertain significance (Oct 16, 2022)
15-23644040-T-G		Inborn genetic diseases	Uncertain significance (Jun 16, 2024)
15-23644041-G-GTCA		MAGEL2-related disorder	Uncertain significance (Sep 04, 2024)
15-23644049-C-T		MAGEL2-related disorder	Uncertain significance (Mar 12, 2024)
15-23644053-C-G		not specified	Conflicting classifications of pathogenicity (Feb 01, 2024)
15-23644060-G-A			Uncertain significance (Jul 22, 2021)
15-23644067-C-G		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
15-23644072-T-C			Uncertain significance (Sep 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGEL2	protein_coding	protein_coding	ENST00000532292	1	2485

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.975	0.0249	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.563	399	369	1.08	0.0000209	4145
Missense in Polyphen		76	73.131	1.0392		861
Synonymous	-1.72	185	158	1.17	0.00000941	1352
Loss of Function	3.75	2	20.2	0.0992	0.00000112	209

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: Probably enhances ubiquitin ligase activity of RING-type zinc finger-containing E3 ubiquitin-protein ligases, possibly through recruitment and/or stabilization of the Ubl-conjugating enzyme (E2) at the E3:substrate complex. Acts as a regulator of retrograde transport via its interaction with VPS35. Recruited to retromer-containing endosomes and promotes the formation of 'Lys- 63'-linked polyubiquitin chains at 'Lys-220' of WASHC1 together with TRIM27, leading to promote endosomal F-actin assembly (PubMed:23452853). Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Significantly promotes the cytoplasmic accumulation of CLOCK (By similarity). {ECO:0000250|UniProtKB:Q9QZ04, ECO:0000269|PubMed:20864041, ECO:0000269|PubMed:23452853}.
• Pathway: Circadian rythm related genes;Prader-Willi and Angelman Syndrome (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.293
• ghis: 0.463

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Magel2
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; taste/olfaction 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); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: Arp2/3 complex-mediated actin nucleation;retrograde transport, endosome to Golgi;regulation of circadian rhythm;negative regulation of transcription, DNA-templated;rhythmic process;protein K63-linked ubiquitination
• Cellular component: nucleus;endosome;early endosome;cytosol;retromer complex
• Molecular function: ubiquitin-protein transferase activity;protein binding