SLC30A9

Chr 4AR

solute carrier family 30 member 9

Also known as: BILAPES, C4orf1, GAC63, HUEL, ZNT9

NCBI Gene: 10463ENSG00000014824UniProt: Q6PML9OMIM: 604604

The protein functions as a mitochondrial proton-coupled zinc antiporter that exports zinc from mitochondria and maintains zinc homeostasis, mitochondrial morphology, and mitochondrial health. Mutations cause Birk-Landau-Perez syndrome, inherited in an autosomal recessive pattern. The gene shows tolerance to loss-of-function variants (LOEUF 0.679), suggesting complete loss of function may be required for disease manifestation.

OMIMResearchSummary from OMIM, UniProt
DNmechanismARLOEUF 0.681 OMIM phenotype
Clinical Summary— SLC30A9
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Gene-Disease Validity (ClinGen)
psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
22 unique Pathogenic / Likely Pathogenic· 59 VUS of 118 total submissions
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.68LOEUF
pLI 0.000
Z-score 3.11
OE 0.45 (0.31–0.68)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.85Z-score
OE missense 0.70 (0.63–0.79)
210 obs / 299.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.45 (0.31–0.68)
0≤0.351.4
Missense OE0.70 (0.63–0.79)
0≤0.61.4
Synonymous OE0.95
0≤1.21.6
LoF obs/exp: 17 / 37.5Missense obs/exp: 210 / 299.9Syn Z: 0.41
DN
0.73top 25%
GOF
0.6247th %ile
LOF
0.3067th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

118 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic4
VUS59
Likely Benign8
Benign9
Conflicting1
18
Pathogenic
4
Likely Pathogenic
59
VUS
8
Likely Benign
9
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
1
16
0
18
Likely Pathogenic
4
0
0
0
4
VUS
0
54
4
1
59
Likely Benign
0
4
0
4
8
Benign
0
3
3
3
9
Conflicting
—1
Total56223899

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC30A9 · 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