MAGED2 (MAGE family member D2)

Gene

• Entrez ID: 10916
• Gene name: MAGE family member D2
• Gene symbol: MAGED2
• Synonyms (NCBI Gene): 11B6, BARTS5, BCG-1, BCG1, HCA10, MAGE-D2
• Chromosome: X
• Chromosome location: Xp11.21
• Summary: This gene is a member of the MAGED gene family. The MAGED genes are clustered on chromosome Xp11. This gene is located in Xp11.2, a hot spot for X-linked intellectual disability (XLID). Mutations in this gene cause a form of transient antenatal Bartter`s

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs875989852	A>G,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs878854404	C>G	Pathogenic	Stop gained, coding sequence variant
rs878854405	A>G	Pathogenic	Splice acceptor variant
rs878854406	TG>-	Pathogenic	Frameshift variant, coding sequence variant
rs1114167295	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT017771	hsa-miR-335-5p	Microarray	18185580
MIRT037133	hsa-miR-877-3p	CLASH	23622248
MIRT2035526	hsa-miR-155	CLIP-seq
MIRT2035527	hsa-miR-2467-3p	CLIP-seq
MIRT2035528	hsa-miR-3678-3p	CLIP-seq
MIRT2035529	hsa-miR-505	CLIP-seq
MIRT2035530	hsa-miR-759	CLIP-seq
MIRT2266027	hsa-miR-3135	CLIP-seq
MIRT2266028	hsa-miR-3677-5p	CLIP-seq
MIRT2266029	hsa-miR-4464	CLIP-seq
MIRT2266030	hsa-miR-4748	CLIP-seq
MIRT2266031	hsa-miR-512-3p	CLIP-seq
MIRT2266032	hsa-miR-604	CLIP-seq
MIRT2266033	hsa-miR-647	CLIP-seq
MIRT2266034	hsa-miR-1185	CLIP-seq
MIRT2266035	hsa-miR-3605-5p	CLIP-seq
MIRT2266036	hsa-miR-3679-5p	CLIP-seq
MIRT2266037	hsa-miR-4303	CLIP-seq
MIRT2266038	hsa-miR-4649-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IBA
GO:0005515	Function	Protein binding	IPI	25852190, 27120771, 32707033
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	IBA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005730	Component	Nucleolus	IDA
GO:0005829	Component	Cytosol	IDA
GO:0007565	Process	Female pregnancy	IMP	27120771
GO:0016020	Component	Membrane	HDA	19946888
GO:0031093	Component	Platelet alpha granule lumen	TAS
GO:0070294	Process	Renal sodium ion absorption	IMP	27120771

Other IDs

• MIM: 300470
• HGNC: 16353
• e!Ensembl: ENSG00000102316

Protein

• UniProt ID: Q9UNF1
• Protein name: Melanoma-associated antigen D2 (11B6) (Breast cancer-associated gene 1 protein) (BCG-1) (Hepatocellular carcinoma-associated protein JCL-1) (MAGE-D2 antigen)
• Protein function: Regulates the expression, localization to the plasma membrane and function of the sodium chloride cotransporters SLC12A1 and SLC12A3, two key components of salt reabsorption in the distal renal tubule.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01454	MAGE	286 → 454	MAGE family	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. In the developing and adult kidney, expressed in the thick ascending limb of the loop of Henle and the distal convoluted tubules outside the loop. {ECO:0000269|PubMed:11856887, ECO:0000269|PubMed:27120771}.
• Sequence:

  MSDTSESGAGLTRFQAEASEKDSSSMMQTLLTVTQNVEVPETPKASKALEVSEDVKVSKA
  SGVSKATEVSKTPEAREAPATQASSTTQLTDTQVLAAENKSLAADTKKQNADPQAVTMPA
  TETKKVSHVADTKVNTKAQETEAAPSQAPADEPEPESAAAQSQENQDTRPKVKAKKARKV
  KHLDGEEDGSSDQSQASGTTGGRRVSKALMASMARRASRGPIAFWARRASRTRLAAWARR
  ALLSLRSPKARRGKARRRAAKLQSSQEPEAPPPRDVALLQGRANDLVKYLLAKDQTKIPI
  KRSDMLKDIIKEYTDVYPEIIERAGYSLEKVFGIQLKEIDKNDHLYILLSTLEPTDAGIL
  GTTKDSPKLGLLMVLLSIIFMNGNRSSEAVIWEVLRKLGLRPGIHHSLFGDVKKLITDEF
  VKQKYLDYARVPNSNPPEYEFFWGLRSYYETSKMKVLKFACKVQKKDPKEWAAQYREAME
  ADLKAAAEAAAEAKARAEIRARMGIGLGSENAAGPCNWDEADIGPWAKARIQAGAEAKAK
  AQESGSASTGASTSTNNSASASASTSGGFSAGASLTATLTFGLFAGLGGAGASTSGSSGA
  CGFSYK

• Sequence length: 606

Pathways

Reactome:

Platelet degranulation

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Bartter disease type 5	Likely pathogenic; Pathogenic	rs2519310187, rs878854404, rs878854405, rs878854406, rs878854407, rs875989852, rs1432384861, rs2519308659	RCV002471619 RCV000211517 RCV000211544 RCV000211479 RCV000211522 RCV000211438 RCV003320417 RCV003484236	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ANTENATAL BARTTER SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME TYPE 5	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CEREBELLAR ATROPHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DANDY-WALKER SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLOBAL DEVELOPMENTAL DELAY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAGED2-related disorder	Benign; Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROTIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TRANSIENT ANTENATAL BARTTER SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Antenatal Bartter syndrome	Antenatal Bartter Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Appendicitis	Appendicitis	BEFREE	16794389		★☆☆☆☆ Found in Text Mining only
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Bartter Disease	Bartter syndrome	BEFREE	27120771, 28134709, 29594084, 29677005		★☆☆☆☆ Found in Text Mining only
Bartter Syndrome	Bartter syndrome	Pubtator	27120771, 27633862, 29146702, 34895150, 36010623, 36359819, 37686237, 38238844	Associate	★☆☆☆☆ Found in Text Mining only
Bartter syndrome antenatal type 1	Bartter syndrome	Pubtator	36359819	Associate	★☆☆☆☆ Found in Text Mining only
Bartter syndrome, antenatal type 1	Bartter syndrome	ORPHANET_DG	27120771		★☆☆☆☆ Found in Text Mining only
BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT	Bartter syndrome	GENOMICS_ENGLAND_DG	27120771		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT	Bartter syndrome	UNIPROT_DG	27120771		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT	Bartter syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BARTTER SYNDROME, TYPE 5, ANTENATAL, TRANSIENT	Bartter syndrome	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	31516568		★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	16424981		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	32941982	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Carcinoma	Colorectal Cancer	BEFREE	25743330		★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Developmental Delay	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Glycogen Storage Disease Type IV	Glycogen storage disease	Pubtator	16502410	Stimulate	★☆☆☆☆ Found in Text Mining only
Glycosuria Renal	Renal glycosuria	Pubtator	36010623	Associate	★☆☆☆☆ Found in Text Mining only
Hypochloremia (disorder)	Hypochloremia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	36010623, 36359819, 37686237	Associate	★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	BEFREE	30541139		★☆☆☆☆ Found in Text Mining only
Kidney Failure, Acute	Kidney Failure	BEFREE	30541139		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	31516568		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	25743330		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29371029		★☆☆☆☆ Found in Text Mining only
Medullary nephrocalcinosis	Medullary nephrocalcinosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	19383316, 22791814		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	19383316, 25724522	Associate	★☆☆☆☆ Found in Text Mining only
Mental Retardation, X-Linked	Mental retardation	BEFREE	11856887		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	14719106, 16424981, 16502410, 16794389, 20648585		★☆☆☆☆ Found in Text Mining only
Nephrogenic Diabetes Insipidus, Type I	Nephrogenic Diabetes Insipidus	BEFREE	28134709		★☆☆☆☆ Found in Text Mining only
Peritonitis	Peritonitis	Pubtator	29733517	Stimulate	★☆☆☆☆ Found in Text Mining only
Sarcoma	Sarcoma	Pubtator	34307667	Stimulate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Stomach Carcinoma	Stomach Carcinoma	BEFREE	25743330		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach Neoplasms	BEFREE	16502410		★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	29733517	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	38128647	Stimulate	★☆☆☆☆ Found in Text Mining only