SLC5A5

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

Basic information

Region (hg38): 19:17871945-17895174

Links

ENSG00000105641NCBI:6528OMIM:601843HGNC:11040Uniprot:Q92911AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • thyroid dyshormonogenesis 1 (Definitive), mode of inheritance: AR
  • thyroid dyshormonogenesis 1 (Strong), mode of inheritance: AR
  • familial thyroid dyshormonogenesis (Supportive), mode of inheritance: AR
  • thyroid dyshormonogenesis 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Thyroid dyshormonogenesis 1AREndocrine; OncologicMedical treatment of hypothyroidism (eg, with T4) can be effective; Thyroid neoplasms have also been reported, and surveillance may be beneficialEndocrine; Oncologic9171822; 19916865; 21543982; 21565787
Neoplasms have been reported as well as endocrine manifestations

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC5A5 gene.

  • not_provided (398 variants)
  • Thyroid_dyshormonogenesis_1 (70 variants)
  • Inborn_genetic_diseases (65 variants)
  • SLC5A5-related_disorder (13 variants)
  • not_specified (13 variants)
  • congenital_hypothyreodism (1 variants)
  • Congenital_hypothyroidism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC5A5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000453.3. 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
2
clinvar
214
clinvar
2
clinvar
218
missense
4
clinvar
7
clinvar
76
clinvar
7
clinvar
94
nonsense
5
clinvar
1
clinvar
6
start loss
0
frameshift
9
clinvar
8
clinvar
17
splice donor/acceptor (+/-2bp)
1
clinvar
16
clinvar
17
Total 19 32 78 221 2

Highest pathogenic variant AF is 0.0000457267

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC5A5protein_codingprotein_codingENST00000222248 1523202
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002950.9971257050431257480.000171
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9183363870.8690.00002544015
Missense in Polyphen120154.080.778811652
Synonymous-0.9551961801.090.00001301425
Loss of Function3.391030.10.3330.00000141322

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004630.000463
Ashkenazi Jewish0.0001110.0000992
East Asian0.0006530.000653
Finnish0.000.00
European (Non-Finnish)0.00006400.0000615
Middle Eastern0.0006530.000653
South Asian0.0001660.000163
Other0.0003330.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Mediates iodide uptake in the thyroid gland.;
Pathway
Thyroid hormone synthesis - Homo sapiens (human);Thyroid hormone synthesis;Thyroxine (Thyroid Hormone) Production;Nuclear Receptors Meta-Pathway;NRF2 pathway;Metabolism of amino acids and derivatives;Tyrosine metabolism;Purine metabolism;Metabolism;Organic anion transporters;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;EGFR1;Thyroxine biosynthesis;Amine-derived hormones (Consensus)

Intolerance Scores

loftool
0.109
rvis_EVS
-0.89
rvis_percentile_EVS
10.43

Haploinsufficiency Scores

pHI
0.0675
hipred
Y
hipred_score
0.591
ghis
0.483

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.248

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc5a5
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
thyroid hormone generation;ion transport;sodium ion transport;iodide transport;transmembrane transport;cellular response to cAMP;cellular response to gonadotropin stimulus
Cellular component
nucleus;plasma membrane;integral component of membrane;extracellular exosome;extracellular vesicle
Molecular function
sodium:iodide symporter activity;iodide transmembrane transporter activity