SLC16A2

solute carrier family 16 member 2, the group of Solute carrier family 16

Basic information

Region (hg38): X:74421493-74533917

Previous symbols: [ "DXS128", "AHDS", "MRX22" ]

Links

ENSG00000147100NCBI:6567OMIM:300095HGNC:10923Uniprot:P36021AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Allan-Herndon-Dudley syndrome (Strong), mode of inheritance: XL
  • Allan-Herndon-Dudley syndrome (Supportive), mode of inheritance: XL
  • Allan-Herndon-Dudley syndrome (Definitive), mode of inheritance: XL
  • Allan-Herndon-Dudley syndrome (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Allan-Herndon-Dudley syndromeXLEndocrine; ObstetricIn affected males, treatment with thyroid hormone has not been described as affecting the neurologic phenotype, but heterozygous women may benefit from monitoring and levothyroxine treatment during pregnancy in order to prevent fetal/neonatal hypothyroidism (regardless of fetal variant status)Craniofacial; Endocrine; Musculoskeletal; Neurologic8484404; 15488219; 14661163; 15889350; 15980113; 18398436; 19194886; 20301789; 20713192; 21098685; 21415082; 21468521

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC16A2 gene.

  • Spastic_paraplegia (197 variants)
  • not_provided (98 variants)
  • Allan-Herndon-Dudley_syndrome (89 variants)
  • Inborn_genetic_diseases (72 variants)
  • not_specified (17 variants)
  • Hereditary_spastic_paraplegia (9 variants)
  • SLC16A2-related_disorder (6 variants)
  • Intellectual_disability (3 variants)
  • History_of_neurodevelopmental_disorder (1 variants)
  • See_cases (1 variants)
  • Prostate_cancer (1 variants)
  • Hypotonia (1 variants)
  • Decreased_activity_of_the_pyruvate_dehydrogenase_complex (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC16A2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006517.5. 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
54
clinvar
9
clinvar
65
missense
10
clinvar
24
clinvar
135
clinvar
31
clinvar
7
clinvar
207
nonsense
19
clinvar
4
clinvar
23
start loss
2
2
frameshift
25
clinvar
11
clinvar
1
clinvar
37
splice donor/acceptor (+/-2bp)
5
clinvar
2
clinvar
7
Total 61 41 138 85 16

Highest pathogenic variant AF is 0.00000495615

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC16A2protein_codingprotein_codingENST00000587091 6112668
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9880.011700000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.381262270.5550.00001823504
Missense in Polyphen2590.9670.274831405
Synonymous0.8898191.80.8820.000007271124
Loss of Function3.39013.40.000.00000100202

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Very active and specific thyroid hormone transporter. Stimulates cellular uptake of thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diidothyronine. Does not transport Leu, Phe, Trp or Tyr. {ECO:0000269|PubMed:23550058, ECO:0000269|PubMed:26426690}.;
Pathway
Thyroid hormone signaling pathway - Homo sapiens (human);Angiopoietin Like Protein 8 Regulatory Pathway;Tyrosine metabolism;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules;Transport of organic anions (Consensus)

Recessive Scores

pRec
0.215

Intolerance Scores

loftool
rvis_EVS
0.1
rvis_percentile_EVS
61.49

Haploinsufficiency Scores

pHI
0.153
hipred
Y
hipred_score
0.662
ghis
0.511

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.187

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc16a2
Phenotype
homeostasis/metabolism phenotype;

Zebrafish Information Network

Gene name
slc16a2
Affected structure
Rohon-Beard neuron
Phenotype tag
abnormal
Phenotype quality
has fewer parts of type

Gene ontology

Biological process
monocarboxylic acid transport;sodium-independent organic anion transport;transmembrane transport;thyroid hormone transport
Cellular component
plasma membrane;integral component of plasma membrane
Molecular function
transporter activity;monocarboxylic acid transmembrane transporter activity;symporter activity;thyroid hormone transmembrane transporter activity