SLC32A1
solute carrier family 32 member 1, the group of Solute carrier family 32
Basic information
Region (hg38): 20:38724486-38729372
Previous symbols: [ "VIAAT" ]
Links
Phenotypes
GenCC
Source:
- developmental and epileptic encephalopathy 114 (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Generalized epilepsy with febrile seizures plus, type 12; Developmental and epileptic encephalopathy 114 | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 34038384; 36073542 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (37 variants)
- not_provided (29 variants)
- Generalized_epilepsy_with_febrile_seizures_plus (8 variants)
- Generalized_epilepsy_with_febrile_seizures_plus,_type_12 (6 variants)
- Intellectual_disability (4 variants)
- Seizure (4 variants)
- Developmental_and_epileptic_encephalopathy_114 (3 variants)
- not_specified (2 variants)
- Developmental_and_epileptic_encephalopathy (2 variants)
- Obesity (1 variants)
- SLC32A1-related_epilepsy (1 variants)
- Mild_global_developmental_delay (1 variants)
- Generalized-onset_seizure (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC32A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080552.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 71 | 79 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 6 | 73 | 1 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC32A1 | protein_coding | protein_coding | ENST00000217420 | 2 | 4911 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.967 | 0.0332 | 125729 | 0 | 3 | 125732 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.30 | 188 | 300 | 0.626 | 0.0000141 | 3404 |
| Missense in Polyphen | 25 | 83.639 | 0.2989 | 997 | ||
| Synonymous | -0.425 | 144 | 138 | 1.05 | 0.00000689 | 1111 |
| Loss of Function | 3.35 | 1 | 15.0 | 0.0668 | 6.55e-7 | 154 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000921 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000881 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the uptake of GABA and glycine into the synaptic vesicles. {ECO:0000250|UniProtKB:O35458}.;
- Pathway
- Benzodiazepine Pathway, Pharmacodynamics;Synaptic vesicle cycle - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);GABAergic synapse - Homo sapiens (human);Nicotine addiction - Homo sapiens (human);Morphine addiction - Homo sapiens (human);Synaptic Vesicle Pathway;GABA receptor Signaling;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Neuronal System;Pyrimidine metabolism;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Bile acid biosynthesis;Porphyrin metabolism;GABA synthesis, release, reuptake and degradation;Neurotransmitter release cycle;Transmission across Chemical Synapses
(Consensus)
Recessive Scores
- pRec
- 0.169
Intolerance Scores
- loftool
- 0.123
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.66
Haploinsufficiency Scores
- pHI
- 0.746
- hipred
- hipred_score
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.386
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc32a1
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype; muscle phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- amino acid transmembrane transport;ion transport;neurotransmitter secretion;aging;gamma-aminobutyric acid transport;glycine transport;hippocampus development;neurotransmitter loading into synaptic vesicle
- Cellular component
- plasma membrane;integral component of synaptic vesicle membrane;dendrite;synaptic vesicle membrane;neuron projection;dendrite terminus;neuron projection terminus;cone cell pedicle;presynaptic active zone;cell tip;inhibitory synapse;clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane;GABA-ergic synapse
- Molecular function
- amino acid transmembrane transporter activity;glycine transmembrane transporter activity;gamma-aminobutyric acid:proton symporter activity