GeneBe

SLC39A4

solute carrier family 39 member 4, the group of Solute carrier family 39

Basic information

Region (hg38): 8:144409742-144416844

Previous symbols: [ "AEZ" ]

Links

ENSG00000147804 ∙ NCBI:55630 ∙ OMIM:607059 ∙ HGNC:17129 ∙ Uniprot:Q6P5W5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • acrodermatitis enteropathica (Strong), mode of inheritance: AR
  • acrodermatitis enteropathica (Strong), mode of inheritance: AR
  • acrodermatitis enteropathica (Strong), mode of inheritance: AR
  • acrodermatitis enteropathica (Supportive), mode of inheritance: AR
  • acrodermatitis enteropathica (Definitive), mode of inheritance: AR
  • acrodermatitis enteropathica (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Acrodermatitis enteropathica, zinc-deficiency typeARBiochemicalThe condition may present with failure to thrive, diarrhea, and dermatitis, and, if untreated, may evolve to include other sequelae of zinc deficiency, including immunodeficiency and neurologic manifestations, and medical management (eg, treatment with oral zinc therapy) can be effectiveBiochemical; Dermatologic; Gastrointestinal4136854; 1090826; 12068297; 19370757; 20883266; 21165302; 21762381; 21906148; 21907902; 22082465; 22166942; 23228939; 23430849
Heterozygous variants have been reported as disease-associated in some reports

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A4 gene.

  • not_provided (799 variants)
  • Hereditary_acrodermatitis_enteropathica (223 variants)
  • Inborn_genetic_diseases (125 variants)
  • SLC39A4-related_disorder (25 variants)
  • not_specified (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000130849.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
13
clinvar
458
clinvar
9
clinvar
 480
missense
7
clinvar
6
clinvar
170
clinvar
22
clinvar
1
clinvar
 206
nonsense
17
clinvar
2
clinvar
1
clinvar
 20
start loss
1
 1
frameshift
45
clinvar
15
clinvar
2
clinvar
 62
splice donor/acceptor (+/-2bp)
1
clinvar
28
clinvar
 29
Total 70 52 186 480 10

Highest pathogenic variant AF is 0.00017728804

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC39A4protein_codingprotein_codingENST00000301305 127154
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0003140.9971256620261256880.000103
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2954123951.040.00002694018
Missense in Polyphen100119.410.837481366
Synonymous-3.752732051.330.00001691417
Loss of Function2.661024.10.4150.00000105262

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.000.00
East Asian0.0001220.000109
Finnish0.00005540.0000462
European (Non-Finnish)0.0002230.000185
Middle Eastern0.0001220.000109
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an important role in cellular zinc homeostasis as a zinc transporter. Regulated in response to zinc availability (By similarity). {ECO:0000250}.;
Pathway
Mineral absorption - Homo sapiens (human);Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;Senescence and Autophagy in Cancer;Zinc influx into cells by the SLC39 gene family;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Metal ion SLC transporters;Zinc transporters (Consensus)

Recessive Scores

pRec
0.127

Intolerance Scores

loftool
0.530
rvis_EVS
1.21
rvis_percentile_EVS
93.05

Haploinsufficiency Scores

pHI
0.0991
hipred
N
hipred_score
0.172
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.231

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Slc39a4
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; vision/eye phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); endocrine/exocrine gland phenotype; muscle phenotype; craniofacial phenotype; cellular phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
cellular zinc ion homeostasis;signal transduction;cellular response to zinc ion starvation;zinc ion import across plasma membrane
Cellular component
plasma membrane;integral component of plasma membrane;apical plasma membrane;cytoplasmic vesicle;recycling endosome membrane
Molecular function
zinc ion transmembrane transporter activity