SLC39A13

Chr 11AR

solute carrier family 39 member 13

Also known as: EDSSPD3, LZT-Hs9, SCDEDS, ZIP13

NCBI Gene: 91252ENSG00000165915UniProt: Q96H72OMIM: 608735

This gene encodes a zinc transporter that transports zinc from the Golgi apparatus to the cytosol, regulating cellular zinc levels. Mutations cause Ehlers-Danlos syndrome, spondylodysplastic type, which involves connective tissue abnormalities with skeletal dysplasia features. The condition follows autosomal recessive inheritance.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismARLOEUF 0.801 OMIM phenotype
Clinical Summary— SLC39A13
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Gene-Disease Validity (ClinGen)
Ehlers-Danlos syndrome, spondylocheirodysplastic type · 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
18 unique Pathogenic / Likely Pathogenic· 150 VUS of 436 total submissions
Explore recent and relevant literature in Research Assistant →
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GeneReview available — SLC39A13
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.80LOEUF
pLI 0.003
Z-score 2.16
OE 0.43 (0.24–0.80)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.26Z-score
OE missense 0.76 (0.67–0.87)
170 obs / 222.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.43 (0.24–0.80)
0≤0.351.4
Missense OE0.76 (0.67–0.87)
0≤0.61.4
Synonymous OE1.03
0≤1.21.6
LoF obs/exp: 7 / 16.5Missense obs/exp: 170 / 222.9Syn Z: -0.28
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveSLC39A13-related spondylodysplastic Ehlers-Danlos syndromeOTHERAR

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

DN
0.7033th %ile
GOF
0.73top 25%
LOF
0.2970th %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

436 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic16
Likely Pathogenic2
VUS150
Likely Benign211
Benign21
Conflicting22
16
Pathogenic
2
Likely Pathogenic
150
VUS
211
Likely Benign
21
Benign
22
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
1
15
0
16
Likely Pathogenic
1
0
1
0
2
VUS
7
123
16
4
150
Likely Benign
0
14
90
107
211
Benign
0
1
19
1
21
Conflicting
—22
Total8139141112422

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

View in ClinVar →

Protein Context — Lollipop Plot

SLC39A13 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 3 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases.
Kumps C et al.·Genes (Basel)
2020Case report
Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway.
Cheng X et al.·J Exp Clin Cancer Res
2021
Phenotypically distinct subtypes of psychosis accompany novel or rare variants in four different signaling genes.
Kranz TM et al.·EBioMedicine
2016
Expanding the clinical and mutational spectrum of B4GALT7-spondylodysplastic Ehlers-Danlos syndrome.
Ritelli M et al.·Orphanet J Rare Dis
2017Case report
Genetic variants affecting mitochondrial function provide further insights for kidney disease.
Cañadas-Garre M et al.·BMC Genomics
2024
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