MAGED2

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

Basic information

Region (hg38): X:54807599-54816015

Links

ENSG00000102316NCBI:10916OMIM:300470HGNC:16353Uniprot:Q9UNF1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Bartter syndrome type 5, antenatal transientXLRenalThe condition can involve prenatal and postnatal manifestations, and awareness may allow medical management of electrolyte abnormalities during the transient period when children are affectedRenal27120771

ClinVar

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

  • not_provided (93 variants)
  • Inborn_genetic_diseases (38 variants)
  • Bartter_disease_type_5 (17 variants)
  • MAGED2-related_disorder (7 variants)
  • Hypoplasia_of_the_corpus_callosum (1 variants)
  • Hypotonia (1 variants)
  • Global_developmental_delay (1 variants)
  • Attention_deficit_hyperactivity_disorder (1 variants)
  • Dandy-Walker_syndrome (1 variants)
  • Cerebellar_atrophy (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. These statistics are base on transcript: NM_000177433.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
17
clinvar
9
clinvar
30
missense
1
clinvar
55
clinvar
9
clinvar
4
clinvar
69
nonsense
5
clinvar
1
clinvar
2
clinvar
8
start loss
0
frameshift
2
clinvar
1
clinvar
1
clinvar
4
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
1
clinvar
5
Total 9 5 63 26 13

Highest pathogenic variant AF is 9.73339e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MAGED2protein_codingprotein_codingENST00000375068 118414
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9950.00462125280011252810.00000399
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.341282270.5630.00001793892
Missense in Polyphen3371.6230.460741336
Synonymous0.5387783.20.9250.000006431223
Loss of Function3.97120.30.04920.00000168343

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00006330.0000471
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Maged2
Phenotype

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