SLC39A13

Chr 11AR

solute carrier family 39 member 13

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

NCBI Gene: 91252ENSG00000165915UniProt: Q96H72

This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]

Primary Disease Associations & Inheritance

Ehlers-Danlos syndrome, spondylodysplastic type, 3MIM #612350
AR
318
ClinVar variants
15
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SLC39A13
🧬
Gene-Disease Validity (ClinGen)
Ehlers-Danlos syndrome, spondylocheirodysplastic type · 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
15 Pathogenic / Likely Pathogenic· 105 VUS of 318 total submissions
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

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.
0.80LOEUF
pLI 0.003
Z-score 2.16
OE 0.43 (0.24–0.80)
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.
1.26Z-score
OE missense 0.76 (0.67–0.87)
170 obs / 222.9 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.0.43 (0.24–0.80)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.76 (0.67–0.87)
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.1.03
0≤1.21.6
LoF obs/exp: 7 / 16.5Missense obs/exp: 170 / 222.9Syn Z: -0.28

ClinVar Variant Classifications

318 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic13
Likely Pathogenic2
VUS105
Likely Benign170
Benign10
Conflicting18
13
Pathogenic
2
Likely Pathogenic
105
VUS
170
Likely Benign
10
Benign
18
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
13
0
13
Likely Pathogenic
0
0
2
0
2
VUS
2
88
15
0
105
Likely Benign
0
13
70
87
170
Benign
0
2
7
1
10
Conflicting
—18
Total210310788318

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.

Gene2Phenotype Curations

SLC39A13-related spondylodysplastic Ehlers-Danlos syndrome

definitive
ARUndeterminedAbsent Gene Product, Altered Gene Product Structure
Dev. DisordersSkeletal
G2P ↗
missense variantinframe deletioninframe insertion

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Ehlers-Danlos syndrome, spondylodysplastic type, 3

MIM #612350

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — SLC39A13
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic variants affecting mitochondrial function provide further insights for kidney disease.
Cañadas-Garre M et al.·BMC Genomics
2024
The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways.
Fukada T et al.·PLoS One
2008Case report
Possible involvement of zinc transporter ZIP13 in myogenic differentiation.
Shoji M et al.·Sci Rep
2024
Broadening the phenotypic spectrum of Beta3GalT6-associated phenotypes.
Leoni C et al.·Am J Med Genet A
2021Case report
Comprehensive analyses of solute carrier family members identify SLC12A2 as a novel therapy target for colorectal cancer.
Chen DY et al.·Sci Rep
2024
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
Expanding the clinical and mutational spectrum of B4GALT7-spondylodysplastic Ehlers-Danlos syndrome.
Ritelli M et al.·Orphanet J Rare Dis
2017Case report
Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13.
Giunta C et al.·Am J Hum Genet
2008Case report
Phenotypically distinct subtypes of psychosis accompany novel or rare variants in four different signaling genes.
Kranz TM et al.·EBioMedicine
2016
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
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