Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	54551
Gene name	MAGE family member L2
Gene symbol	MAGEL2
Synonyms (NCBI Gene)	NDNL1PWLSSHFYNGnM15
Chromosome	15
Chromosome location	15q11.2
Summary	Prader-Willi syndrome (PWS) is caused by the loss of expression of imprinted genes in chromosome 15q11-q13 region. Affected individuals exhibit neonatal hypotonia, developmental delay, and childhood-onset obesity. Necdin (NDN), a gene involved in the term

Show/Hide all (42)

SNP ID	Visualize variation	Clinical significance	Consequence
rs2233061	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs34875116	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, synonymous variant, coding sequence variant
rs115892604	C>G	Benign, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs146970674	C>G,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs398122415	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs398122416	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs398122417	AT>-	Pathogenic	Coding sequence variant, frameshift variant
rs398122418	G>A	Pathogenic	Coding sequence variant, stop gained
rs528108868	ATCGGCTGTGCAGGTGGGGCC>-,ATCGGCTGTGCAGGTGGGGCCATCGGCTGTGCAGGTGGGGCC	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe insertion, inframe deletion
rs570335069	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs752097874	G>A,C,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs760039339	C>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs770374710	G>-,GG	Pathogenic	Frameshift variant, coding sequence variant
rs771501846	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs781777662	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs794726941	GGGTGGGGCCTGGCGGATCACGGGTGGGGCCTGGCGGATCAC>-,GGGTGGGGCCTGGCGGATCAC	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion
rs797044883	G>A	Pathogenic, likely-pathogenic	Coding sequence variant, stop gained
rs866419580	G>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs869312694	C>A	Pathogenic	Coding sequence variant, stop gained
rs886041598	G>T	Pathogenic	Coding sequence variant, stop gained
rs886041955	->A	Pathogenic	Frameshift variant, coding sequence variant
rs1060499934	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs1249139977	G>A,C	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs1250752332	->TG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1350074368	T>C,G	Likely-pathogenic	Initiator codon variant, missense variant
rs1386125417	GTGGGGCCTGGCGGATCACAG>-	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, inframe deletion
rs1432429004	TC>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555374117	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1555374125	CA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1555374227	A>-	Pathogenic	Coding sequence variant, frameshift variant
rs1555374254	->C	Pathogenic	Coding sequence variant, frameshift variant
rs1555374290	G>A	Pathogenic	Stop gained, coding sequence variant
rs1555374335	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1566783684	C>T	Pathogenic	Coding sequence variant, stop gained
rs1566784441	C>T	Pathogenic	Coding sequence variant, stop gained
rs1595331427	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1595331599	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1595332359	T>-	Pathogenic	Coding sequence variant, frameshift variant
rs1595332462	GCCTGCAAGACTGCAGGCGGTGCCTG>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1595332731	G>T	Pathogenic	Coding sequence variant, stop gained
rs1595334202	GGCAGG>CAGGGGCC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1595334203	->G	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (35)

miRTarBase ID	miRNA	Experiments	Reference
MIRT525999	hsa-miR-4760-3p	PAR-CLIP	22012620
MIRT525998	hsa-miR-6858-3p	PAR-CLIP	22012620
MIRT525997	hsa-miR-664a-3p	PAR-CLIP	22012620
MIRT525996	hsa-miR-4719	PAR-CLIP	22012620
MIRT525995	hsa-miR-513b-5p	PAR-CLIP	22012620
MIRT525993	hsa-miR-5696	PAR-CLIP	22012620
MIRT525994	hsa-miR-579-3p	PAR-CLIP	22012620
MIRT525992	hsa-miR-664b-3p	PAR-CLIP	22012620
MIRT525991	hsa-miR-513c-5p	PAR-CLIP	22012620
MIRT525990	hsa-miR-514b-5p	PAR-CLIP	22012620
MIRT525996	hsa-miR-4719	PAR-CLIP	27292025
MIRT525999	hsa-miR-4760-3p	PAR-CLIP	27292025
MIRT525995	hsa-miR-513b-5p	PAR-CLIP	27292025
MIRT525991	hsa-miR-513c-5p	PAR-CLIP	27292025
MIRT525990	hsa-miR-514b-5p	PAR-CLIP	27292025
MIRT525993	hsa-miR-5696	PAR-CLIP	27292025
MIRT525994	hsa-miR-579-3p	PAR-CLIP	27292025
MIRT525997	hsa-miR-664a-3p	PAR-CLIP	27292025
MIRT525992	hsa-miR-664b-3p	PAR-CLIP	27292025
MIRT525998	hsa-miR-6858-3p	PAR-CLIP	27292025
MIRT525999	hsa-miR-4760-3p	PAR-CLIP	22012620
MIRT525998	hsa-miR-6858-3p	PAR-CLIP	22012620
MIRT525997	hsa-miR-664a-3p	PAR-CLIP	22012620
MIRT525996	hsa-miR-4719	PAR-CLIP	22012620
MIRT525995	hsa-miR-513b-5p	PAR-CLIP	22012620
MIRT525993	hsa-miR-5696	PAR-CLIP	22012620
MIRT525994	hsa-miR-579-3p	PAR-CLIP	22012620
MIRT525992	hsa-miR-664b-3p	PAR-CLIP	22012620
MIRT525991	hsa-miR-513c-5p	PAR-CLIP	22012620
MIRT525990	hsa-miR-514b-5p	PAR-CLIP	22012620
MIRT2035542	hsa-miR-320a	CLIP-seq
MIRT2035543	hsa-miR-320b	CLIP-seq
MIRT2035544	hsa-miR-320c	CLIP-seq
MIRT2035545	hsa-miR-320d	CLIP-seq
MIRT2035546	hsa-miR-4429	CLIP-seq

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0004842	Function	Ubiquitin-protein transferase activity	IMP	23452853
GO:0005515	Function	Protein binding	IPI	20864041, 23452853, 26365382, 32296183
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IDA	23452853
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IEA
GO:0005829	Component	Cytosol	IEA
GO:0030904	Component	Retromer complex	IDA	23452853
GO:0034314	Process	Arp2/3 complex-mediated actin nucleation	IDA	23452853
GO:0042147	Process	Retrograde transport, endosome to Golgi	IDA	23452853
GO:0042752	Process	Regulation of circadian rhythm	IEA
GO:0042752	Process	Regulation of circadian rhythm	ISS
GO:0045892	Process	Negative regulation of DNA-templated transcription	IEA
GO:0045892	Process	Negative regulation of DNA-templated transcription	ISS
GO:0048511	Process	Rhythmic process	IEA
GO:0051127	Process	Positive regulation of actin nucleation	IEA
GO:0070534	Process	Protein K63-linked ubiquitination	IMP	23452853

MIM	HGNC	e!Ensembl
605283	6814	ENSG00000254585

Q9UJ55

Protein name

MAGE-like protein 2 (Necdin-like protein 1) (Protein nM15)

Protein 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 o

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01454	MAGE	1027 → 1195	MAGE family	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in placenta, fetal and adult brain. Not detected in heart and small intestine, very low levels in fibroblasts. Not expressed in brain of a Prader-Willi patient. {ECO:0000269|PubMed:10915770}.

Sequence

MSQLSKNLGDSSPPAEAPKPPVYSRPTVLMRAPPASSRAPPVPWDPPPIDLQASLAAWQA
PQPAWEAPQGQLPAPVVPMTQPPALGGPIVPAPPLGGPMGKPPTPGVLMVHPPPPGAPMA
QPPTPGVLMVHPSAPGAPMAHPPPPGTPMSHPPPPGTPMAHPPPPGTPMAHPPPPGTPMV
HPPPPGTPMAHPPPPGTPMAHPPPPGTPMAHPPPPGTPMAHPPPPGTPMAQPPAPGVLMA
QPLTPGVLMVQPAAPGAPMVQPPPAAMMTQPQPSGAPMAKPPGPGVLMIHPPGARAPMTQ
PPASGAPMAQPAAPPAQPMAPPAQPMASWAPQAQPLILQIQSQVIRAPPQVPQGPQAPPA
QLATPPGWQATSPGWQATQQGWQATPLTWQTTQVTWQAPAVTWQVPPPMRQGPPPIRPGP
PPIRPGPPPVRQAPPLIRQAPPVIRQAPPVIRQAPPVIRQAPAVIRQAPPVIRQAPPVIR
QAPPVIRQAPPLIRQAPPPIRPAPQVLATQPPLWQALPPPPPLRQAPQARLPAPQVQAAP
QVPTAPPATQVPAAPPAGPQVPQPVLPAPLSAPLSAPQAVHCPSIIWQAPKGQPPVPHEI
PTSMEFQEVQQTQALAWQAQKAPTHIWQPLPAQEAQRQAPPLVQLEQPFQGAPPSQKAVQ
IQLPPQQAQASGPQAEVPTLPLQPSWQAPPAVLQAQPGPPVAAANFPLGSAKSLMTPSGE
CRASSIDRRGSSKERRTSSKERRAPSKDRMIFAATFCAPKAVSAARAHLPAAWKNLPATP
ETFAPSSSVFPATSQFQPASLNAFKGPSAASETPKSLPYALQDPFACVEALPAVPWVPQP
NMNASKASQAVPTFLMATAAAPQATATTQEASKTSVEPPRRSGKATRKKKHLEAQEDSRG
HTLAFHDWQGPRPWENLNLSDWEVQSPIQVSGDWEHPNTPRGLSGWEGPSTSRILSGWEG
PSASWALSAWEGPSTSRALGLSESPGSSLPVVVSEVASVSPGSSATQDNSKVEAQPLSPL
DERANALVQFLLVKDQAKVPVQRSEMVKVILREYKDECLDIINRANNKLECAFGYQLKEI
DTKNHAYIIINKLGYHTGNLVASYLDRPKFGLLMVVLSLIFMKGNCVREDLIFNFLFKLG
LDVRETNGLFGNTKKLITEVFVRQKYLEYRRIPYTEPAEYEFLWGPRAFLETSKMLVLRF
LAKLHKKDPQSWPFHYLEALAECEWEDTDEDEPDTGDSAHGPTSRPPPR

Sequence length

1249

Interactions

View interactions

379

Show/Hide Causal Diseases (13)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ambiguous genitalia	Pathogenic	rs770374710	RCV001257380
Developmental disorder	Likely pathogenic; Pathogenic	rs2140719261, rs2503978535	RCV001843715 RCV003127423
Generalized hypotonia	Pathogenic	rs770374710	RCV001257380
Intellectual disability	Likely pathogenic; Pathogenic	rs1890387347	RCV001260888
MAGEL2-related disorder	Likely pathogenic; Pathogenic	rs797044883	RCV003407693
Multiple joint contractures	Pathogenic	rs770374710	RCV001257380
Neurodevelopmental delay	Pathogenic	rs770374710	RCV002273971
Neurodevelopmental disorder	Pathogenic	rs770374710	RCV002277321
Prader-Willi syndrome	Pathogenic; Likely pathogenic	rs2140713056, rs2140714298, rs797044883, rs1890356742	RCV002250101 RCV002250102 RCV000762935 RCV001195825
Prader-Willi-like syndrome	Pathogenic	rs770374710	RCV003458348
Schaaf-Yang syndrome	Pathogenic; Likely pathogenic	rs899176705, rs2140711872, rs2140713406, rs2140717041, rs2140717180, rs2140718089, rs2140714112, rs2140719261, rs1267004913, rs768844200, rs2140715275, rs2503980170, rs770374710, rs797044883, rs869312694 View all (23 more)	RCV001376011 RCV001420183 RCV001420187 RCV001420188 RCV001420184 RCV001420185 RCV001775427 RCV005253897 RCV002245531 RCV002251026 RCV002255785 RCV002465451 RCV000170356 RCV000508676 RCV000209903 RCV003147142 RCV003223523 RCV001782757 RCV003314286 RCV003387609 RCV003457223 RCV004586405 RCV000455050 RCV000508606 RCV000508643 RCV000508613 RCV000754908 RCV000754907 RCV000853315 RCV000989269 RCV001090063 RCV000074484 RCV000074485 RCV000074486 RCV000074487 RCV001249368 RCV001251169 RCV003315258 RCV001420186
See cases	Pathogenic	rs770374710	RCV002252015
Ventriculomegaly	Pathogenic	rs770374710	RCV001257380

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Autism spectrum disorder	Uncertain significance	rs2503982926	RCV003127422
Genetic developmental and epileptic encephalopathy	Benign; Likely benign	rs2233069	RCV005626674

Show/Hide Text Mining Associations (44)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	34951053
Anxiety	Stimulate	33076953
Arthrogryposis	Associate	26365340, 28281571, 31504653, 31791363, 33820833
Autism Spectrum Disorder	Associate	24076603, 27195816, 34265304
Autistic Disorder	Associate	24076603
Body Dysmorphic Disorders	Associate	31504653
Bone Diseases Developmental	Associate	33820833
Carcinoma Hepatocellular	Associate	32941982
Cicatrix Hypertrophic	Associate	30320389
Contracture	Associate	27195816
Cryptorchidism	Associate	34128869
Developmental Disabilities	Associate	27195816, 31504653
Disorders of Sex Development	Associate	34128869
Dwarfism Pituitary	Associate	31504653
Dyskinesia Drug Induced	Associate	34128869
Dyspnea	Associate	29581464
Feeding and Eating Disorders	Associate	27195816
Fetal akinesia syndrome X linked	Associate	27195816
Fever	Associate	31791363
Growth Disorders	Associate	34128869
Hypersensitivity Delayed	Associate	29581464
Hypopituitarism	Associate	31504653
Intellectual Disability	Associate	24076603, 26365340, 27195816, 34128869
Intellectual Disability	Stimulate	33076953
Language Disorders	Associate	34128869
MASA (Mental Retardation Aphasia Shuffling Gait Adducted Thumbs) Syndrome	Associate	31504653
Mental Disorders	Stimulate	33076953
Muscle Hypotonia	Associate	27195816, 31791363
Neoplasms	Associate	34951053
Neurobehavioral Manifestations	Associate	27195816
Neuroblastoma	Associate	39217334
Obesity	Associate	31791363, 34128869
Obesity	Stimulate	33076953
Paranoid Disorders	Associate	29343559
Pituitary Diseases	Associate	31504653
Prader Willi Syndrome	Associate	16286533, 20631049, 24076603, 26365340, 28281571, 29343559, 30302899, 31791363, 32480405, 34128869, 34265304, 34389046, 35343647, 36243518, 37343528, 37533374 View all (1 more)
Puberty Precocious	Associate	34630334
Schaaf Yang syndrome	Associate	26365340, 27195816, 28281571, 29581464, 30302899, 31504653, 31791363, 33076953, 33371171, 34128869, 34265304, 34389046, 35343647, 36243518, 37343528, 37533374 View all (1 more)
Schizophrenia	Associate	29343559
Sexual Dysfunctions Psychological	Stimulate	33076953
Sleep Apnea Syndromes	Associate	31504653
Sleep Wake Disorders	Stimulate	33076953
Vision Disorders	Associate	31504653
Yang Deficiency	Associate	34128869

MAGEL2 (MAGE family member L2)