SLC12A5

Chr 20ADAR

solute carrier family 12 member 5

Also known as: DEE34, EIEE34, EIG14, KCC2, hKCC2

The encoded protein is a neuronal potassium-chloride cotransporter that maintains low intracellular chloride levels required for proper GABA-mediated inhibition and is involved in dendritic spine formation and maturation. Mutations cause developmental and epileptic encephalopathy 34 and idiopathic generalized epilepsy through both autosomal dominant and autosomal recessive inheritance patterns. The gene is highly intolerant to loss-of-function variants, and disease predominantly results from haploinsufficiency, though the dual inheritance patterns suggest variant-dependent mechanisms of pathogenicity.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismAD/ARLOEUF 0.142 OMIM phenotypes
Clinical SummarySLC12A5
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Gene-Disease Validity (ClinGen)
developmental and epileptic encephalopathy · ARLimited

Limited evidence — not for standalone diagnostic reporting

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

Dual constrained — LoF & missense intolerant
LoF Constraint
0.14LOEUF
pLI 1.000
Z-score 6.58
OE 0.05 (0.020.14)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
4.70Z-score
OE missense 0.50 (0.460.55)
347 obs / 696.1 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.05 (0.020.14)
00.351.4
Missense OE0.50 (0.460.55)
00.61.4
Synonymous OE0.92
01.21.6
LoF obs/exp: 3 / 56.3Missense obs/exp: 347 / 696.1Syn Z: 1.01
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongSLC12A5-related epilepsy of infancy with migrating focal seizuresOTHERAR
Mechanism Note (expert annotation)
LOF

KCC2 potassium-chloride cotransporter. LOF variants reduce chloride extrusion capacity, impairing GABAergic inhibition and causing DEE. GOF is not an established mechanism.

References:PMID:26028587

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

DN
0.5180th %ile
GOF
0.75top 25%
LOF
0.48top 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

SLC12A5 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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