SLC38A4

solute carrier family 38 member 4, the group of Solute carrier family 38

Basic information

Region (hg38): 12:46764761-46832408

Links

ENSG00000139209 ∙ NCBI:55089 ∙ OMIM:608065 ∙ HGNC:14679 ∙ Uniprot:Q969I6 ∙ 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 SLC38A4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC38A4 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					1	1
missense			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	1

Variants in SLC38A4

This is a list of pathogenic ClinVar variants found in the SLC38A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-46766725-A-T		not specified	Uncertain significance (Jun 17, 2024)
12-46766756-A-G		not specified	Uncertain significance (Apr 15, 2024)
12-46766759-C-G		not specified	Uncertain significance (Oct 19, 2024)
12-46768314-A-G		not specified	Uncertain significance (Nov 25, 2024)
12-46768329-C-G		not specified	Uncertain significance (Oct 25, 2022)
12-46769332-C-T		not specified	Uncertain significance (Nov 20, 2023)
12-46769333-A-C		not specified	Uncertain significance (Sep 12, 2024)
12-46769388-G-C		not specified	Uncertain significance (Aug 12, 2022)
12-46769413-T-G		not specified	Uncertain significance (Oct 26, 2022)
12-46775108-T-C		not specified	Uncertain significance (Nov 20, 2023)
12-46775135-C-T		not specified	Uncertain significance (Jul 30, 2024)
12-46775165-C-T		not specified	Uncertain significance (Nov 09, 2024)
12-46776979-C-T		not specified	Uncertain significance (Jun 29, 2022)
12-46776996-C-T		not specified	Likely benign (Mar 07, 2023)
12-46778506-A-G		not specified	Uncertain significance (Mar 26, 2024)
12-46778539-C-T		not specified	Uncertain significance (Dec 16, 2023)
12-46778547-T-G		not specified	Uncertain significance (Sep 11, 2024)
12-46778571-T-C		not specified	Likely benign (Feb 27, 2023)
12-46778607-C-T		not specified	Uncertain significance (Apr 26, 2024)
12-46778649-T-A		not specified	Uncertain significance (Sep 17, 2021)
12-46778662-A-C		not specified	Uncertain significance (Mar 19, 2024)
12-46784569-C-A		not specified	Uncertain significance (Aug 16, 2021)
12-46788026-G-A			Benign (Mar 29, 2018)
12-46788529-T-A		not specified	Uncertain significance (Sep 22, 2023)
12-46788532-T-A		not specified	Uncertain significance (Oct 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC38A4	protein_coding	protein_coding	ENST00000447411	15	67646

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.560	0.440	125660	0	7	125667	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	225	298	0.755	0.0000147	3588
Missense in Polyphen		64	114.09	0.56098		1368
Synonymous	0.758	93	103	0.905	0.00000513	1041
Loss of Function	3.92	6	28.7	0.209	0.00000150	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000665	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-dependent amino acid transporter. Mediates electrogenic symport of neutral amino acids and sodium ions. Has a broad specificity, with a preference for Ala, followed by His, Cys, Asn, Ser, Gly, Val, Thr, Gln and Met. May mediate sodium- independent transport of cationic amino acids, such as Arg and Lys. Amino acid uptake is pH-dependent, with low transport activities at pH 6.5, intermediate at pH 7.0 and highest between pH 7.5 and 8.5. {ECO:0000269|PubMed:11342143, ECO:0000269|PubMed:11414754}.
• Pathway: Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;Glucose-Alanine Cycle;Chlorthalidone Action Pathway;Trichlormethiazide Action Pathway;Iminoglycinuria;Lysinuric Protein Intolerance;Blue diaper syndrome;Lysinuric protein intolerance (LPI);Cystinuria;Indapamide Action Pathway;Furosemide Action Pathway;Torsemide Action Pathway;Hartnup Disorder;Glucose Transporter Defect (SGLT2);Kidney Function;Glucose Transporter Defect (SGLT2);Metolazone Action Pathway;Hydrochlorothiazide Action Pathway;Cyclothiazide Action Pathway;Hydroflumethiazide Action Pathway;Chlorothiazide Action 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;Lipoate metabolism;Histidine metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Valine, leucine and isoleucine degradation;Aminosugars metabolism;Bile acid biosynthesis;Glycerophospholipid metabolism;Porphyrin metabolism;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.699
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc38a4

Gene ontology

• Biological process: amino acid transmembrane transport;sodium ion transport;amino acid transport
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: amino acid transmembrane transporter activity;symporter activity