SLC38A9

solute carrier family 38 member 9, the group of Solute carrier family 38

Basic information

Region (hg38): 5:55625844-55773194

Links

ENSG00000177058 ∙ NCBI:153129 ∙ OMIM:616203 ∙ HGNC:26907 ∙ Uniprot:Q8NBW4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• lysosomal storage disease (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC38A9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A9 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	1

Variants in SLC38A9

This is a list of pathogenic ClinVar variants found in the SLC38A9 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-55626526-C-T		not specified	Uncertain significance (Feb 14, 2023)
5-55626541-T-C		not specified	Uncertain significance (Jan 04, 2022)
5-55626547-C-T		not specified	Likely benign (Jul 13, 2022)
5-55626601-T-C		not specified	Uncertain significance (Dec 20, 2023)
5-55633764-T-C		not specified	Likely benign (Feb 16, 2023)
5-55633770-C-T		not specified	Uncertain significance (Dec 21, 2023)
5-55633782-C-T		not specified	Uncertain significance (Nov 14, 2023)
5-55633797-G-A		not specified	Uncertain significance (Dec 21, 2023)
5-55633866-A-G		not specified	Uncertain significance (Sep 01, 2021)
5-55635617-G-A		not specified	Uncertain significance (Dec 14, 2023)
5-55635632-A-C		not specified	Uncertain significance (Sep 23, 2023)
5-55645805-T-C		not specified	Uncertain significance (May 20, 2024)
5-55645869-T-A			Benign (Mar 29, 2018)
5-55649222-C-T		not specified	Uncertain significance (Jan 31, 2024)
5-55649258-C-T		not specified	Uncertain significance (Apr 01, 2024)
5-55652618-G-C		not specified	Uncertain significance (Dec 22, 2023)
5-55652711-C-G		not specified	Uncertain significance (Mar 07, 2024)
5-55656732-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-55656740-T-C		not specified	Uncertain significance (Oct 26, 2023)
5-55664749-A-G		not specified	Uncertain significance (Dec 16, 2023)
5-55664761-A-G		not specified	Uncertain significance (Mar 25, 2024)
5-55669240-G-A		not specified	Uncertain significance (Dec 30, 2023)
5-55669267-A-G		not specified	Uncertain significance (May 06, 2022)
5-55669302-A-G		not specified	Uncertain significance (Aug 17, 2021)
5-55669582-A-G		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A9	protein_coding	protein_coding	ENST00000396865	14	147350

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.286	0.714	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	222	293	0.757	0.0000141	3712
Missense in Polyphen		68	86.837	0.78307		1136
Synonymous	1.26	85	101	0.841	0.00000505	1042
Loss of Function	3.59	6	25.6	0.235	0.00000108	343

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000278	0.000278
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000979	0.000979
Finnish	0.00	0.00
European (Non-Finnish)	0.0000732	0.0000703
Middle Eastern	0.000979	0.000979
South Asian	0.000101	0.0000980
Other	0.000186	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysosomal amino acid transporter involved in the activation of mTORC1 in response to amino acids. Probably acts as an amino acid sensor of the Rag GTPases and Ragulator complexes, 2 complexes involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids (PubMed:25561175, PubMed:25567906). Following activation by amino acids, the Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated. SLC38A9 mediates transport of amino acids with low capacity and specificity with a slight preference for polar amino acids, suggesting that it acts as an amino acid sensor instead (PubMed:25561175, PubMed:25567906). The high concentration of arginine in lysosomes suggests that it acts as an arginine sensor (PubMed:25567906). {ECO:0000269|PubMed:25561175, ECO:0000269|PubMed:25567906}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Transcriptional Regulation by TP53;Intracellular signaling by second messengers (Consensus)

Intolerance Scores

• loftool: 0.749
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.106
• hipred: Y
• hipred_score: 0.595
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a9

Gene ontology

• Biological process: amino acid transmembrane transport;cell cycle arrest;regulation of macroautophagy;positive regulation of TOR signaling;cellular response to amino acid stimulus
• Cellular component: nucleoplasm;lysosome;lysosomal membrane;late endosome;integral component of membrane;intracellular membrane-bounded organelle;Ragulator complex
• Molecular function: protein binding;amino acid transmembrane transporter activity