GeneBe

SLC25A1

solute carrier family 25 member 1, the group of Solute carrier family 25

Basic information

Region (hg38): 22:19175581-19178739

Previous symbols: [ "SLC20A3" ]

Links

ENSG00000100075 ∙ NCBI:6576 ∙ OMIM:190315 ∙ HGNC:10979 ∙ Uniprot:P53007 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • myasthenic syndrome, congenital, 23, presynaptic (Strong), mode of inheritance: AR
  • myasthenic syndrome, congenital, 23, presynaptic (Strong), mode of inheritance: AR
  • presynaptic congenital myasthenic syndrome (Supportive), mode of inheritance: AD
  • D,L-2-hydroxyglutaric aciduria (Supportive), mode of inheritance: AR
  • D,L-2-hydroxyglutaric aciduria (Limited), mode of inheritance: AR
  • D,L-2-hydroxyglutaric aciduria (Strong), mode of inheritance: AR
  • myasthenic syndrome, congenital, 23, presynaptic (Strong), mode of inheritance: AR
  • mitochondrial disease (Definitive), mode of inheritance: AR
  • D,L-2-hydroxyglutaric aciduria (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myasthenic syndrome, congenital, 23, presynapticARGeneralMedical management (with 3,4-DAP) has been reported as beneficialNeurologic10963100; 23393310; 23561848; 26870663; 31527857; 31808147

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC25A1 gene.

  • not_provided (161 variants)
  • Inborn_genetic_diseases (28 variants)
  • not_specified (26 variants)
  • SLC25A1-related_disorder (12 variants)
  • 2-hydroxyglutaric_aciduria (8 variants)
  • Myasthenic_syndrome,_congenital,_23,_presynaptic (7 variants)
  • D,L-2-hydroxyglutaric_aciduria (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC25A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005984.5. 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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
38
clinvar
1
clinvar
 44
missense
1
clinvar
10
clinvar
69
clinvar
 80
nonsense
1
clinvar
1
clinvar
1
clinvar
 3
start loss
0
frameshift
4
clinvar
2
clinvar
 6
splice donor/acceptor (+/-2bp)
2
clinvar
2
clinvar
 4
Total 8 15 75 38 1

Highest pathogenic variant AF is 0.000066957145

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SLC25A1protein_codingprotein_codingENST00000215882 93249
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.05880.9381257200241257440.0000954
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.241281740.7360.00001051967
Missense in Polyphen3453.9750.62992555
Synonymous-1.018372.11.150.00000428644
Loss of Function2.58516.20.3098.80e-7171

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001450.000145
Ashkenazi Jewish0.000.00
East Asian0.00005620.0000544
Finnish0.000.00
European (Non-Finnish)0.0001440.000141
Middle Eastern0.00005620.0000544
South Asian0.00003270.0000327
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in citrate-H(+)/malate exchange. Important for the bioenergetics of hepatic cells as it provides a carbon source for fatty acid and sterol biosyntheses, and NAD(+) for the glycolytic pathway.;
Disease
DISEASE: Combined D-2- and L-2-hydroxyglutaric aciduria (D2L2AD) [MIM:615182]: An autosomal recessive neurometabolic disorder characterized by neonatal-onset encephalopathy with severe muscular weakness, intractable seizures, respiratory distress, and lack of psychomotor development resulting in early death. Brain imaging shows abnormalities including enlarged ventricles, delayed myelination, and germinal layer cysts. {ECO:0000269|PubMed:23561848, ECO:0000269|PubMed:27306203}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism of carbohydrates;Metabolism of lipids;Fatty acyl-CoA biosynthesis;Glycolysis and Gluconeogenesis;Metabolism;Fatty acid metabolism;TCA cycle;Gluconeogenesis;Glucose metabolism (Consensus)

Recessive Scores

pRec
0.321

Intolerance Scores

loftool
0.330
rvis_EVS
-0.52
rvis_percentile_EVS
21.2

Haploinsufficiency Scores

pHI
0.381
hipred
Y
hipred_score
0.760
ghis
0.508

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.999

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Slc25a1
Phenotype

Zebrafish Information Network

Gene name
slc25a1a
Affected structure
intestine
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
gluconeogenesis;mitochondrial citrate transmembrane transport;fatty-acyl-CoA biosynthetic process
Cellular component
nucleus;mitochondrial inner membrane;integral component of membrane;extracellular exosome
Molecular function
citrate transmembrane transporter activity;tricarboxylic acid transmembrane transporter activity