SLC39A10

Chr 2

solute carrier family 39 member 10

Also known as: LZT-Hs2, ZIP10

NCBI Gene: 57181 ENSG00000196950 UniProt: Q9ULF5 OMIM: 608733

This protein functions as a zinc-influx transporter that forms heterodimers with SLC39A6 to mediate cellular zinc uptake, playing essential roles in mitosis initiation and B-cell maintenance. Mutations cause autosomal recessive developmental delays, intellectual disability, and seizures, typically with onset in infancy or early childhood. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely incompatible with normal development.

OMIM ResearchSummary from RefSeq, UniProt

Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A10 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

OMIM ResearchGenerating clinical summary…

LOEUF 0.28

Clinical Summary— SLC39A10

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.99). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

74 VUS of 96 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.28LOEUF

pLI 0.993

Z-score 4.37

OE 0.11 (0.05–0.28)

Highly constrained

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

Missense Constraint?

1.95Z-score

OE missense 0.74 (0.68–0.81)

334 obs / 450.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.11 (0.05–0.28)

0≤0.351.4

Missense OE?0.74 (0.68–0.81)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 3 / 27.9Missense obs/exp: 334 / 450.7Syn Z: -0.01

ClinVar Variant Classifications

96 submitted variants in ClinVar

ClinVar

Classification Summary

VUS74

Likely Benign9

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	74	74
Likely Benign	9	9
Benign	0	0
Total	83	83

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

View in ClinVar →

33 pathogenic / likely-pathogenic (of 38) ClinVar copy-number / structural variants overlap SLC39A10 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →