SLC30A10

Chr 1AR

solute carrier family 30 member 10

Also known as: HMDPC, HMNDYT1, ZNT10, ZNT8, ZRC1, ZnT-10

NCBI Gene: 55532ENSG00000196660UniProt: Q6XR72

This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleomorphic phenotype, including dystonia and adult-onset parkinsonism. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]

Primary Disease Associations & Inheritance

Hypermanganesemia with dystonia 1MIM #613280
AR
346
ClinVar variants
42
Pathogenic / LP
0.98
pLI score· haploinsufficient
0
Active trials
Clinical Summary— SLC30A10
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
42 Pathogenic / Likely Pathogenic· 156 VUS of 346 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
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.
0.25LOEUF
pLI 0.980
Z-score 3.20
OE 0.00 (0.00–0.25)
Highly constrained

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

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.
1.58Z-score
OE missense 0.73 (0.65–0.82)
197 obs / 269.8 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.0.00 (0.00–0.25)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.73 (0.65–0.82)
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.0.98
0≤1.21.6
LoF obs/exp: 0 / 11.9Missense obs/exp: 197 / 269.8Syn Z: 0.13

ClinVar Variant Classifications

346 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic37
Likely Pathogenic5
VUS156
Likely Benign106
Benign32
Conflicting10
37
Pathogenic
5
Likely Pathogenic
156
VUS
106
Likely Benign
32
Benign
10
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
3
1
33
0
37
Likely Pathogenic
1
1
3
0
5
VUS
1
120
34
1
156
Likely Benign
0
5
31
70
106
Benign
0
0
32
0
32
Conflicting
—10
Total512713371346

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC30A10 · 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

Hypermanganesemia with dystonia 1

MIM #613280

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — SLC30A10
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genotype-Phenotype Relations for the Dystonia-Parkinsonism Genes GLB1, SLC6A3, SLC30A10, SLC39A14, and PLA2G6: MDSGene Systematic Review.
Rodriguez-Antiguedad J et al.·Int J Mol Sci
2025Review
Genetic Disorders of Manganese Metabolism.
Anagianni S et al.·Curr Neurol Neurosci Rep
2019Review
Manganese and the brain.
Tuschl K et al.·Int Rev Neurobiol
2013Review
Forced Overexpression and Knockout Analysis of SLC30A and SLC39A Family Genes Suggests Their Involvement in Establishing Resistance to Cisplatin in Human Cancer Cells.
Kamynina M et al.·Int J Mol Sci
2024
A rare genetic variant in the manganese transporter SLC30A10 and elevated liver enzymes in the general population.
Seidelin AS et al.·Hepatol Int
2022
Mutations in SLC30A10 cause parkinsonism and dystonia with hypermanganesemia, polycythemia, and chronic liver disease.
Quadri M et al.·Am J Hum Genet
2012
GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms.
Ward LD et al.·Nat Commun
2021
A case of dystonia with polycythemia and hypermanganesemia caused by SLC30A10 mutation: a treatable inborn error of manganese metabolism.
Tavasoli A et al.·BMC Pediatr
2019Review
Removal of Toxic Metabolites-Chelation: Manganese Disorders.
Vogt H et al.·J Inherit Metab Dis
2025Review
Atypical Neurologic Phenotype and Novel SLC30A10 Mutation in Two Brothers with Hereditary Hypermanganesemia.
Gulab S et al.·Neuropediatrics
2018Case report
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

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools