MAGED2

MAGE family member D2, the group of MAGE family|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): X:54807598-54816015

Links

ENSG00000102316 ∙ NCBI:10916 ∙ OMIM:300470 ∙ HGNC:16353 ∙ Uniprot:Q9UNF1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bartter disease type 5 (Strong), mode of inheritance: XL
• antenatal Bartter syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bartter syndrome type 5, antenatal transient	XL	Renal	The condition can involve prenatal and postnatal manifestations, and awareness may allow medical management of electrolyte abnormalities during the transient period when children are affected	Renal	27120771

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MAGED2 gene.

• not provided (73 variants)
• Inborn genetic diseases (12 variants)
• Bartter disease type 5 (10 variants)
• MAGED2-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MAGED2 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	7	11	19
missense		1	22	3	5	31
nonsense	1	1	2			4
start loss						0
frameshift			1			1
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)	1	2				3
splice region			2	1		3
non coding			4	4	16	24
Total	2	4	31	14	33

Variants in MAGED2

This is a list of pathogenic ClinVar variants found in the MAGED2 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-54809253-G-T			Likely benign (Sep 01, 2020)
X-54809737-A-G			Uncertain significance (May 22, 2023)
X-54809804-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2023)
X-54809806-A-G			Benign/Likely benign (Nov 13, 2023)
X-54809883-C-T			Benign (Jun 26, 2022)
X-54809901-T-C			Benign (Jan 25, 2024)
X-54809927-C-T		Inborn genetic diseases	Uncertain significance (Aug 19, 2023)
X-54809928-A-G		Bartter disease type 5	Benign (Jan 31, 2024)
X-54809938-C-T		Bartter disease type 5	Pathogenic (Aug 14, 2023)
X-54809966-C-G			Uncertain significance (Sep 26, 2023)
X-54809979-T-C			Uncertain significance (Dec 03, 2022)
X-54809985-AGCTGACACCAAGAAACAGAAT-A			Uncertain significance (Jan 06, 2021)
X-54810014-C-T			Likely benign (Jun 04, 2022)
X-54810017-A-G			Benign (Aug 17, 2023)
X-54810019-G-C			Uncertain significance (Feb 09, 2023)
X-54810020-C-T		Inborn genetic diseases	Uncertain significance (Nov 10, 2022)
X-54810053-T-A		Inborn genetic diseases	Uncertain significance (Sep 25, 2023)
X-54810059-ATG-A		Bartter disease type 5	Pathogenic (Sep 23, 2016)
X-54810072-A-G		Bartter disease type 5	Benign (Jan 31, 2024)
X-54810073-A-T		Bartter disease type 5	Pathogenic (Sep 23, 2016)
X-54810125-C-A		MAGED2-related disorder • Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 09, 2023)
X-54810133-C-T			Uncertain significance (Apr 25, 2022)
X-54810156-C-T			Benign (Jan 23, 2024)
X-54810182-G-A		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
X-54810837-G-C			Benign (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MAGED2	protein_coding	protein_coding	ENST00000375068	11	8414

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00462	125280	0	1	125281	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	128	227	0.563	0.0000179	3892
Missense in Polyphen		33	71.623	0.46074		1336
Synonymous	0.538	77	83.2	0.925	0.00000643	1223
Loss of Function	3.97	1	20.3	0.0492	0.00000168	343

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	0.0000633	0.0000471
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: 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. {ECO:0000269|PubMed:27120771}.
• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.513
• hipred: N
• hipred_score: 0.496
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Maged2

Gene ontology

• Biological process: platelet degranulation;female pregnancy;renal sodium ion absorption
• Cellular component: extracellular region;nucleus;nucleolus;cytosol;membrane;platelet alpha granule lumen
• Molecular function: protein binding