SLC38A1

solute carrier family 38 member 1, the group of Solute carrier family 38

Basic information

Region (hg38): 12:46183063-46270017

Links

ENSG00000111371

∙ NCBI:81539 ∙ OMIM:608490 ∙ HGNC:13447 ∙ Uniprot:Q9H2H9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A1 gene.

not_specified (33 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030674.4. 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 clinvar	1
missense			33 clinvar			33
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	33	0	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A1	protein_coding	protein_coding	ENST00000398637	15	86955

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.931	0.0693	124754	0	6	124760	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.15	168	267	0.630	0.0000139	3188
Missense in Polyphen		42	102.48	0.40983		1285
Synonymous	0.365	96	101	0.954	0.00000584	921
Loss of Function	4.01	4	26.1	0.153	0.00000128	338

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000652	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000446	0.0000442
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Functions as a sodium-dependent amino acid transporter. Mediates the saturable, pH-sensitive and electrogenic cotransport of glutamine and sodium ions with a stoichiometry of 1:1. May also transport small zwitterionic and aliphatic amino acids with a lower affinity. May supply glutamatergic and GABAergic neurons with glutamine which is required for the synthesis of the neurotransmitters glutamate and GABA. {ECO:0000269|PubMed:10891391}.;
Pathway: GABAergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Astrocytic Glutamate-Glutamine Uptake And Metabolism;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Synaptic Vesicle Pathway;Biopterin metabolism;Amino acid transport across the plasma membrane;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;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Valine, leucine and isoleucine degradation;Aminosugars metabolism;Bile acid biosynthesis;Glycerophospholipid metabolism;Neurotransmitter uptake and metabolism In glial cells;Transmission across Chemical Synapses;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

pRec: 0.148

Intolerance Scores

loftool: 0.175
rvis_EVS: -0.38
rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

pHI: 0.569
hipred: Y
hipred_score: 0.768
ghis: 0.607

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.523

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Slc38a1
Phenotype

Gene ontology

Biological process: neurotransmitter uptake;amino acid transmembrane transport;sodium ion transport;amino acid transport;neutral amino acid transport;L-alpha-amino acid transmembrane transport
Cellular component: plasma membrane;integral component of plasma membrane;integral component of membrane;extracellular exosome
Molecular function: amino acid:sodium symporter activity;protein binding;amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity