SLC13A5

Chr 17

solute carrier family 13 member 5

Also known as: DEE25, EIEE25, INDY, NACT, mIndy

NCBI Gene: 284111ENSG00000141485UniProt: Q86YT5

This protein is a sodium-dependent citrate cotransporter that regulates cellular metabolic processes by transporting citrate across cell membranes. Biallelic mutations cause developmental and epileptic encephalopathy 25 with amelogenesis imperfecta, characterized by early infantile epileptic encephalopathy and defective tooth enamel formation. The condition follows autosomal recessive inheritance with pathogenicity resulting from loss of protein function.

ResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismLOEUF 0.67
Clinical Summary— SLC13A5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
46 unique Pathogenic / Likely Pathogenic· 160 VUS of 500 total submissions
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Clinical Trials
3 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.67LOEUF
pLI 0.001
Z-score 2.83
OE 0.39 (0.24–0.67)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.14Z-score
OE missense 0.83 (0.75–0.91)
288 obs / 347.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.39 (0.24–0.67)
0≤0.351.4
Missense OE0.83 (0.75–0.91)
0≤0.61.4
Synonymous OE1.02
0≤1.21.6
LoF obs/exp: 10 / 25.4Missense obs/exp: 288 / 347.9Syn Z: -0.16
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSLC13A5-related epileptic encephalopathy with seizure onset in the first days of lifeLOFAR

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

DN
0.85top 10%
GOF
0.77top 25%
LOF
0.1895th %ile

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.

ClinVar Variant Classifications

500 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic32
Likely Pathogenic14
VUS160
Likely Benign271
Benign18
Conflicting2
32
Pathogenic
14
Likely Pathogenic
160
VUS
271
Likely Benign
18
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
20
0
12
0
32
Likely Pathogenic
12
2
0
0
14
VUS
3
141
14
2
160
Likely Benign
0
2
129
140
271
Benign
0
0
18
0
18
Conflicting
—2
Total35145173142497

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SLC13A5 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients