MDGA2

Chr 14AR

MAM domain containing glycosylphosphatidylinositol anchor 2

Also known as: DEE122, MAMDC1, c14_5286

Predicted to be involved in regulation of synapse organization and spinal cord motor neuron differentiation. Predicted to act upstream of or within several processes, including motor behavior; negative regulation of neuron apoptotic process; and neuron migration. Predicted to be located in extracellular region and plasma membrane. Predicted to be active in GABA-ergic synapse; glutamatergic synapse; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 0.241 OMIM phenotype
Clinical SummaryMDGA2
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint?
0.24LOEUF
pLI 0.999
Z-score 5.14
OE 0.10 (0.050.24)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
1.68Z-score
OE missense 0.76 (0.690.84)
306 obs / 400.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.10 (0.050.24)
00.351.4
Missense OE?0.76 (0.690.84)
00.61.4
Synonymous OE?0.91
01.21.6
LoF obs/exp: 4 / 38.3Missense obs/exp: 306 / 400.4Syn Z: 0.83
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateMDGA2-related developmental and epileptic encephalopathy with abnormal cranial MRILOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.3991th %ile
GOF
0.4678th %ile
LOF
0.66top 25%

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

MDGA2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →