SLC16A1
protein-codingsolute carrier family 16 member 1, the group of Solute carrier family 16
Gene summary
The protein encoded by this gene is a proton-linked monocarboxylate transporter that catalyzes the movement of many monocarboxylates, such as lactate and pyruvate, across the plasma membrane. Mutations in this gene are associated with erythrocyte lactate transporter defect. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Oct 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019223
Submitter: Ambry Genetics
Inheritance Pattern: SD
Disease ID:MONDO:0014490
Submitter: Ambry Genetics
Inheritance Pattern: SD
Disease ID:MONDO:0014490
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014490
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014490
Submitter: Ambry Genetics
Inheritance Pattern: Unknown
Disease ID:MONDO:0012396
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: Unknown
Disease ID:MONDO:0009501
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014490
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0014490
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0012396
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0012396
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Biochemical; Endocrine; Musculoskeletal; Neurologic; Renal
Intervention: Biochemical; Endocrine; Musculoskeletal; Renal
Rationale: In Hyperinsulinemic hypoglycemia, familial, several affected individuals have reported as manifesting with severe sequelae, such as hypoglycemia-induced seizures, which could potentially be averted by early recognition and treatment; In Erythrocyte lactate transporter defect, exercise and heat exposure may result in sequelae such as rhabdomyolysis, and precautions may be beneficial; In Monocarboxylate transporter 1 deficiency, ensuring adequate caloric intake has been reported as beneficial to decrease the frequency of episodes of ketoacidotic episodes, and medical management (eg, with intravenous glucose or dextrose and bicarbonate) of episodes has been described as effective in terms of immediate management, and related long-term sequelae
Comments: Depending on the allelic condition, manifestations in dominant conditions may involve primarily endocrine or musculoskeletal/renal manifestations
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC16A1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003051.4. 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 | 4 | 71 | 1 | 76 | ||
| missense | 2 | 160 | 12 | 174 | ||
| nonsense | 5 | 4 | 1 | 10 | ||
| start loss | 0 | |||||
| frameshift | 5 | 6 | 2 | 13 | ||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 10 | 12 | 167 | 83 | 1 | 273 |
Highest pathogenic variant AF is 0.0000142527115
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003042.3 | 4 | MANE Select | |
| Ensembl | ENSP00000358640.4 | 4 | MANE Select | |
| RefSeq | NP_001159968.1 | 4 | Standard | |
| Ensembl | ENSP00000397106.2 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Warburg Effect
- Glutaminolysis and Cancer
- Photodynamic therapy-induced HIF-1 survival signaling
- Pyruvate metabolism
- Pyruvate metabolism and Citric Acid (TCA) cycle
Biological Process
- pyruvate metabolic process
- lipid metabolic process
- centrosome cycle
- monocarboxylic acid transport
- mevalonate transport
Molecular Function
- monocarboxylic acid transmembrane transporter activity
- lactate transmembrane transporter activity
- mevalonate transmembrane transporter activity
- symporter activity
- protein homodimerization activity
Cellular Component
- centrosome
- plasma membrane
- integral component of plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000538576
- Coding exons
- 4
- Length
- 45167
- Individuals with no LoFs
- 125732
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 16
- Defined
- 125748
- p
- 0.0000636
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 193 | 269 | 0.716 | 0.0000138 | 3238 |
| Missense (PolyPhen) | 32 | 87.179 | 0.36706 | 1022 | ||
| Synonymous | -1.09 | 118 | 104 | 1.14 | 0.00000593 | 1038 |
| Loss of Function | 2.12 | 8 | 17.6 | 0.455 | 0.00000117 | 203 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.00016 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Proton-coupled 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. Depending on the tissue and on cicumstances, mediates the import or export of lactic acid and ketone bodies. Required for normal nutrient assimilation, increase of white adipose tissue and body weight gain when on a high-fat diet. Plays a role in cellular responses to a high-fat diet by modulating the cellular levels of lactate and pyruvate, small molecules that contribute to the regulation of central metabolic pathways and insulin secretion, with concomitant effects on plasma insulin levels and blood glucose homeostasis. {ECO:0000269|PubMed:17701893}.;
- Disease
- DISEASE: Familial hyperinsulinemic hypoglycemia 7 (HHF7) [MIM:610021]: Dominantly inherited hypoglycemic disorder characterized by inappropriate insulin secretion during anaerobic exercise or on pyruvate load. {ECO:0000269|PubMed:17701893}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Monocarboxylate transporter 1 deficiency (MCT1D) [MIM:616095]: A metabolic disorder characterized by recurrent ketoacidosis, a pathologic state due to ketone formation exceeding ketone utilization. The clinical consequences of ketoacidosis are vomiting, osmotic diuresis, dehydration, and Kussmaul breathing. The condition may progress to decreased consciousness and, ultimately, death. {ECO:0000269|PubMed:25390740}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- LoFtool
- 0.173
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.35
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.901
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |