SLC16A3
protein-codingsolute carrier family 16 member 3, the group of Solute carrier family 16|MicroRNA protein coding host genes
Gene summary
Lactic acid and pyruvate transport across plasma membranes is catalyzed by members of the proton-linked monocarboxylate transporter (MCT) family, which has been designated solute carrier family-16. Each MCT appears to have slightly different substrate and inhibitor specificities and transport kinetics, which are related to the metabolic requirements of the tissues in which it is found. The MCTs, which include MCT1 (SLC16A1; MIM 600682) and MCT2 (SLC16A7; MIM 603654), are characterized by 12 predicted transmembrane domains (Price et al., 1998 [PubMed 9425115]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC16A3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004207.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 5 | 1 | 7 | ||
| missense | 94 | 10 | 1 | 105 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 97 | 15 | 2 | 114 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004198.1 | 4 | MANE Select | |
| Ensembl | ENSP00000462405.1 | 4 | MANE Select | |
| RefSeq | NP_001035887.1 | 4 | Standard | |
| RefSeq | NP_001035888.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- pyruvate metabolic process
- monocarboxylic acid transport
- plasma membrane lactate transport
- leukocyte migration
Molecular Function
- RNA binding
- protein binding
- monocarboxylic acid transmembrane transporter activity
- lactate transmembrane transporter activity
- symporter activity
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
- nuclear membrane
- parallel fiber to Purkinje cell synapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000581287
- Coding exons
- 4
- Length
- 32733
- Individuals with no LoFs
- 125481
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 35
- Defined
- 125516
- p
- 0.000139
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0506 | 311 | 309 | 1.01 | 0.0000218 | 2956 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00015 | 0.00014 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- -0.64
- RVIS percentile EVS
- 16.68
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |