SLC16A1

protein-coding

solute 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

NM_003051.4

Inheritance

AD, SD, AR

ClinVar variants

P:22U:167B:84

Top phenotype

Hyperinsulinemic hypoglycemia, familial, 7; Erythrocyte lactate transporter defect; Monocarboxylate transporter 1 deficiency

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr1:112,911,847-112,957,593

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~45.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

disorder of fatty acid and ketone body metabolismLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0019223

Submitter: Ambry Genetics

ketoacidosis due to monocarboxylate transporter-1 deficiencyMODERATE

Inheritance Pattern: SD

Disease ID:MONDO:0014490

Submitter: Ambry Genetics

ketoacidosis due to monocarboxylate transporter-1 deficiencySTRONG

Inheritance Pattern: SD

Disease ID:MONDO:0014490

Submitter: PanelApp Australia

ketoacidosis due to monocarboxylate transporter-1 deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014490

Submitter: Labcorp Genetics (formerly Invitae)

ketoacidosis due to monocarboxylate transporter-1 deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014490

Submitter: Ambry Genetics

exercise-induced hyperinsulinismLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0012396

Submitter: Labcorp Genetics (formerly Invitae)

metabolic myopathy due to lactate transporter defectLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0009501

Submitter: Labcorp Genetics (formerly Invitae)

ketoacidosis due to monocarboxylate transporter-1 deficiencySTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014490

Submitter: Labcorp Genetics (formerly Invitae)

ketoacidosis due to monocarboxylate transporter-1 deficiencySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014490

Submitter: Orphanet

exercise-induced hyperinsulinismSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012396

Submitter: PanelApp Australia

exercise-induced hyperinsulinismSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012396

Submitter: Orphanet

Clinical Genomic Database (CGD)

Hyperinsulinemic hypoglycemia, familial, 7; Erythrocyte lactate transporter defect; Monocarboxylate transporter 1 deficiencyAD/AR

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

Refs: 3775384; 3395513; 3395514; 1358043; 10590411; 11207177; 12502513; 17701893; 25390740; 25865495Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC16A1 variants in ClinVar

9 Conditions Cataloged
not providedTotal: 256
Inborn genetic diseasesTotal: 43
Exercise-induced hyperinsulinismTotal: 30
not specifiedTotal: 27
SLC16A1-related disorderTotal: 24
Ketoacidosis due to monocarboxylate transporter-1 deficiencyTotal: 12
Metabolic myopathy due to lactate transporter defectTotal: 6
Monocarboxylate transporter 1 deficiency, autosomal dominantTotal: 5

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
71
clinvar
1
clinvar
76
missense
2
clinvar
160
clinvar
12
clinvar
174
nonsense
5
clinvar
4
clinvar
1
clinvar
10
start loss
0
frameshift
5
clinvar
6
clinvar
2
clinvar
13
splice donor/acceptor (+/-2bp)
0
Total1012167831273

Highest pathogenic variant AF is 0.0000142527115

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 40 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003051.4RefSeqNP_003042.34MANE Select
ENST00000369626.8EnsemblENSP00000358640.44MANE Select
NM_001166496.2RefSeqNP_001159968.14Standard
ENST00000429288.2EnsemblENSP00000397106.24Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.651932690.7160.00001383238
Missense (PolyPhen)3287.1790.367061022
Synonymous-1.091181041.140.000005931038
Loss of Function2.12817.60.4550.00000117203

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000870.000087rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish0.000140.00014rare
European (Non-Finnish)0.0000350.000035rare
South Asian0.000160.00013rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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