GeneBe

SLC39A5

solute carrier family 39 member 5, the group of Solute carrier family 39

Basic information

Region (hg38): 12:56230049-56237846

Links

ENSG00000139540 ∙ NCBI:283375 ∙ OMIM:608730 ∙ HGNC:20502 ∙ Uniprot:Q6ZMH5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • myopia 24, autosomal dominant (Strong), mode of inheritance: AD
  • myopia 24, autosomal dominant (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myopia 24ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic24891338

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC39A5 gene.

  • not_specified (88 variants)
  • not_provided (19 variants)
  • Myopia_24,_autosomal_dominant (12 variants)
  • SLC39A5-related_disorder (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC39A5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000173596.3. 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
7
clinvar
2
clinvar
 9
missense
1
clinvar
82
clinvar
13
clinvar
5
clinvar
 101
nonsense
2
clinvar
1
clinvar
 3
start loss
0
frameshift
2
clinvar
1
clinvar
 3
splice donor/acceptor (+/-2bp)
3
clinvar
 3
Total 3 2 87 20 7

Highest pathogenic variant AF is 0.000018588651

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC39A5protein_codingprotein_codingENST00000266980 107798
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.38e-110.25112544013061257470.00122
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2383103220.9630.00001903342
Missense in Polyphen136128.921.05491428
Synonymous0.4031481540.9590.000009111315
Loss of Function0.8331822.20.8090.00000130213

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001950.00195
Ashkenazi Jewish0.001240.00109
East Asian0.0007610.000761
Finnish0.0007050.000647
European (Non-Finnish)0.001550.00149
Middle Eastern0.0007610.000761
South Asian0.001050.000948
Other0.001890.00179

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a role in polarized cells by carrying out serosal-to-mucosal zinc transport. Plays a role in eye development. Could regulate the BMP/TGF-beta (bone morphogenetic protein/transforming growth factor-beta) signaling pathway and modulates extracellular matrix (ECM) proteins of the sclera (PubMed:24891338). Seems to play a central role in controlling organismal zinc status (By similarity). {ECO:0000250|UniProtKB:Q9D856, ECO:0000269|PubMed:24891338}.;
Disease
DISEASE: Myopia 24, autosomal dominant (MYP24) [MIM:615946]: A refractive error of the eye, in which parallel rays from a distant object come to focus in front of the retina, vision being better for near objects than for far. {ECO:0000269|PubMed:24891338, ECO:0000269|PubMed:25525168}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Nuclear Receptors Meta-Pathway;NRF2 pathway;Zinc homeostasis;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)

Intolerance Scores

loftool
0.909
rvis_EVS
-0.37
rvis_percentile_EVS
28.2

Haploinsufficiency Scores

pHI
0.131
hipred
N
hipred_score
0.170
ghis
0.416

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.146

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc39a5
Phenotype
homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; skeleton phenotype; immune system phenotype; liver/biliary system phenotype;

Gene ontology

Biological process
eye development;cellular zinc ion homeostasis;BMP signaling pathway;cellular response to zinc ion starvation;positive regulation of mRNA splicing, via spliceosome;neural precursor cell proliferation;G1 to G0 transition involved in cell differentiation;zinc ion import across plasma membrane
Cellular component
integral component of plasma membrane;basolateral plasma membrane;extracellular exosome
Molecular function
molecular_function;zinc ion transmembrane transporter activity