SLC16A3

solute carrier family 16 member 3, the group of Solute carrier family 16|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:82217933-82261129

Links

ENSG00000141526 ∙ NCBI:9123 ∙ OMIM:603877 ∙ HGNC:10924 ∙ Uniprot:O15427 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC16A3 gene.

• Inborn genetic diseases (35 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC16A3 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	1	5
missense			33	2	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	6	2

Variants in SLC16A3

This is a list of pathogenic ClinVar variants found in the SLC16A3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-82236016-G-T		not specified	Uncertain significance (Jun 06, 2023)
17-82236045-G-A		not specified	Likely benign (Dec 20, 2022)
17-82236052-C-T			Benign (Jul 05, 2018)
17-82236078-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-82236194-G-C		not specified	Uncertain significance (Apr 25, 2023)
17-82236199-C-T		not specified	Uncertain significance (Jul 13, 2022)
17-82236756-G-A		not specified	Uncertain significance (Dec 21, 2023)
17-82236772-C-T			Likely benign (Jul 05, 2018)
17-82236802-G-A			Likely benign (Aug 01, 2022)
17-82236831-G-A		not specified	Uncertain significance (Jun 21, 2022)
17-82236870-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-82237264-C-T		not specified	Uncertain significance (Nov 08, 2021)
17-82237290-T-G		not specified	Uncertain significance (Aug 14, 2023)
17-82237305-G-A		not specified	Uncertain significance (Oct 10, 2023)
17-82237341-T-G		not specified	Uncertain significance (Apr 12, 2022)
17-82237360-T-C		not specified	Uncertain significance (Apr 13, 2022)
17-82237378-C-T		not specified	Uncertain significance (Sep 07, 2022)
17-82237396-G-A		not specified	Uncertain significance (May 11, 2022)
17-82237402-C-G		not specified	Uncertain significance (Feb 09, 2023)
17-82237416-C-T		not specified	Uncertain significance (Jun 17, 2022)
17-82237417-G-A		not specified	Uncertain significance (May 09, 2023)
17-82237422-C-A		not specified	Uncertain significance (Jul 25, 2023)
17-82237473-G-A		not specified	Uncertain significance (Nov 22, 2022)
17-82237504-C-T		not specified	Uncertain significance (Aug 30, 2021)
17-82237587-A-G		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC16A3	protein_coding	protein_coding	ENST00000581287	4	32733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000294	0.812	125481	0	35	125516	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0506	311	309	1.01	0.0000218	2956
Missense in Polyphen		130	159.35	0.81583		1612
Synonymous	-3.95	214	152	1.41	0.0000125	1033
Loss of Function	1.17	7	11.2	0.623	5.53e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000145	0.000141
Middle Eastern	0.000219	0.000218
South Asian	0.000196	0.000196
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proton-linked monocarboxylate transporter. Catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate (By similarity). {ECO:0000250}.
• Pathway: Central carbon metabolism in cancer - Homo sapiens (human);Pyruvate metabolism;Pyruvate metabolism and Citric Acid (TCA) cycle;Bile salt and organic anion SLC transporters;The citric acid (TCA) cycle and respiratory electron transport;Glycolysis and Gluconeogenesis;Metabolism;Proton-coupled monocarboxylate transport;Transport of bile salts and organic acids, metal ions and amine compounds;SLC-mediated transmembrane transport;Transport of small molecules;Butanoate metabolism;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.68

Haploinsufficiency Scores

• pHI: 0.214
• hipred: Y
• hipred_score: 0.754
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.965

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc16a3

Gene ontology

• Biological process: pyruvate metabolic process;monocarboxylic acid transport;plasma membrane lactate transport;leukocyte migration
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;nuclear membrane;parallel fiber to Purkinje cell synapse;integral component of postsynaptic density membrane
• Molecular function: RNA binding;protein binding;monocarboxylic acid transmembrane transporter activity;lactate transmembrane transporter activity;symporter activity