SLC30A9

Chr 4AR

solute carrier family 30 member 9

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

NCBI Gene: 10463ENSG00000014824UniProt: Q6PML9

Enables zinc ion transmembrane transporter activity. Involved in intracellular zinc ion homeostasis; regulation of mitochondrion organization; and zinc ion transport. Located in several cellular components, including cytoplasmic vesicle; endoplasmic reticulum; and mitochondrial membrane. [provided by Alliance of Genome Resources, Jul 2025]

Primary Disease Associations & Inheritance

Birk-Landau-Perez syndromeMIM #617595
AR
98
ClinVar variants
22
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— SLC30A9
🧬
Gene-Disease Validity (ClinGen)
psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
22 Pathogenic / Likely Pathogenic· 58 VUS of 98 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.68LOEUF
pLI 0.000
Z-score 3.11
OE 0.45 (0.31–0.68)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.85Z-score
OE missense 0.70 (0.63–0.79)
210 obs / 299.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.45 (0.31–0.68)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.70 (0.63–0.79)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.95
0≤1.21.6
LoF obs/exp: 17 / 37.5Missense obs/exp: 210 / 299.9Syn Z: 0.41

ClinVar Variant Classifications

98 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic4
VUS58
Likely Benign8
Benign9
Conflicting1
18
Pathogenic
4
Likely Pathogenic
58
VUS
8
Likely Benign
9
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
18
0
18
Likely Pathogenic
3
0
1
0
4
VUS
0
53
4
1
58
Likely Benign
0
4
0
4
8
Benign
0
3
3
3
9
Conflicting
—1
Total36026898

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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Birk-Landau-Perez syndrome

MIM #617595

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Defining mitochondrial protein functions through deep multiomic profiling.
Rensvold JW et al.·Nature
2022
Clinical Phenotype in Individuals With Birk-Landau-Perez Syndrome Associated With Biallelic SLC30A9 Pathogenic Variants.
Steel DBD et al.·Neurology
2023
N-acetyltransferase 10 facilitates tumorigenesis of diffuse large B-cell lymphoma by regulating AMPK/mTOR signalling through N4-acetylcytidine modification of SLC30A9.
Ding M et al.·Clin Transl Med
2024
SLC30A9: an evolutionarily conserved mitochondrial zinc transporter essential for mammalian early embryonic development.
Ge J et al.·Cell Mol Life Sci
2024
PRDM1-driven SLC30A9 overexpression contributes to the malignant phenotype of cervical cancer cells via promoting mitochondrial hyperfunction.
Wang H et al.·Cell Death Dis
2025
Exome and Genome Sequencing Reveals Novel Variants for Severe Diabetic Retinopathy in Type 1 Diabetes.
Vuori N et al.·Invest Ophthalmol Vis Sci
2025
Human genetic adaptation related to cellular zinc homeostasis.
Roca-Umbert A et al.·PLoS Genet
2023
Expanding the Phenotype of Syndromic SLC30A9 -Associated Disease.
Wagner NE et al.·Am J Med Genet A
2026Case report
Genome-wide association analyses of common infections in a large practice-based biobank.
Jiang L et al.·BMC Genomics
2022
Signatures of Evolutionary Adaptation in Quantitative Trait Loci Influencing Trace Element Homeostasis in Liver.
Engelken J et al.·Mol Biol Evol
2016
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
4 Weeks Supplementation of Huel Ready to Eat Foods

The Effect of Huel on Markers of Inflammation

ACTIVE NOT RECRUITING
NCT07049874Phase NANewcastle UniversityStarted 2025-02-01
Huel

External Resources

Links to major genomics databases and tools