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

ENSG00000147100

∙ NCBI:6567 ∙ OMIM:300095 ∙ HGNC:10923 ∙ Uniprot:P36021 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Allan-Herndon-Dudley syndrome	XL	Endocrine; Obstetric	In 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; Neurologic	8484404; 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC16A2	protein_coding	protein_coding	ENST00000587091	6	112668

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0117	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.38	126	227	0.555	0.0000182	3504
Missense in Polyphen		25	90.967	0.27483		1405
Synonymous	0.889	81	91.8	0.882	0.00000727	1124
Loss of Function	3.39	0	13.4	0.00	0.00000100	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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