SLC7A5

solute carrier family 7 member 5, the group of Solute carrier family 7|MicroRNA protein coding host genes|CD molecules

Basic information

Region (hg38): 16:87830016-87869507

Links

ENSG00000103257 ∙ NCBI:8140 ∙ OMIM:600182 ∙ HGNC:11063 ∙ Uniprot:Q01650 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A5 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				4	6	10
missense			27	2	2	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				2	1	3
Total	0	0	27	8	9

Variants in SLC7A5

This is a list of pathogenic ClinVar variants found in the SLC7A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-87832961-G-C		SLC7A5-related disorder	Likely benign (May 24, 2019)
16-87832984-G-T		not specified	Uncertain significance (Aug 21, 2023)
16-87832995-A-T		not specified	Uncertain significance (Sep 26, 2023)
16-87834417-T-C		not specified	Uncertain significance (Dec 16, 2023)
16-87834419-C-A		not specified	Uncertain significance (Jan 22, 2024)
16-87834422-T-C		not specified	Uncertain significance (Aug 23, 2021)
16-87834456-C-A		not specified	Uncertain significance (Jun 23, 2021)
16-87834535-G-C		SLC7A5-related disorder	Benign (Dec 23, 2019)
16-87834540-C-T		not specified	Uncertain significance (Mar 01, 2023)
16-87834579-G-C		not specified	Uncertain significance (Jun 30, 2022)
16-87834582-C-T		not specified	Uncertain significance (Aug 14, 2023)
16-87836492-G-T		SLC7A5-related disorder	Likely benign (May 02, 2019)
16-87836522-C-A		not specified	Uncertain significance (Sep 20, 2022)
16-87836548-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-87836644-C-G		not specified	Uncertain significance (May 17, 2023)
16-87836651-G-T		SLC7A5-related disorder	Likely benign (Jul 10, 2019)
16-87837853-C-T		not specified	Uncertain significance (May 20, 2024)
16-87837854-G-A		SLC7A5-related disorder	Benign (Dec 31, 2019)
16-87837861-G-A		Autism spectrum disorder	Uncertain significance (Dec 01, 2016)
16-87838708-G-A			Benign (Dec 11, 2017)
16-87838749-G-A			Benign (May 31, 2018)
16-87838767-G-A		SLC7A5-related disorder	Likely benign (Jun 12, 2019)
16-87838793-C-T		not specified	Uncertain significance (Dec 28, 2022)
16-87839704-C-T		not specified	Uncertain significance (Dec 20, 2023)
16-87839721-G-A		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A5	protein_coding	protein_coding	ENST00000261622	10	39466

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.235	0.765	125717	0	14	125731	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	215	295	0.730	0.0000181	3208
Missense in Polyphen		76	133.47	0.56941		1493
Synonymous	-4.42	213	145	1.47	0.0000105	1102
Loss of Function	3.17	5	20.4	0.245	9.07e-7	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.0000570	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-independent, high-affinity transport of large neutral amino acids such as phenylalanine, tyrosine, leucine, arginine and tryptophan, when associated with SLC3A2/4F2hc. Involved in cellular amino acid uptake. Acts as an amino acid exchanger. Involved in the transport of L-DOPA across the blood- brain barrier, and that of thyroid hormones triiodothyronine (T3) and thyroxine (T4) across the cell membrane in tissues such as placenta. Plays a role in neuronal cell proliferation (neurogenesis) in brain. Involved in the uptake of methylmercury (MeHg) when administered as the L-cysteine or D,L-homocysteine complexes, and hence plays a role in metal ion homeostasis and toxicity. Involved in the cellular activity of small molecular weight nitrosothiols, via the stereoselective transport of L- nitrosocysteine (L-CNSO) across the transmembrane. May play an important role in high-grade gliomas. Mediates blood-to-retina L- leucine transport across the inner blood-retinal barrier which in turn may play a key role in maintaining large neutral amino acids as well as neurotransmitters in the neural retina. Acts as the major transporter of tyrosine in fibroblasts. When associated with LAPTM4B, recruits SLC3A2 and SLC7A5 to lysosomes to promote leucine uptake into these organelles and is required for mTORC1 activation (PubMed:25998567). {ECO:0000269|PubMed:10049700, ECO:0000269|PubMed:10391915, ECO:0000269|PubMed:10574970, ECO:0000269|PubMed:11311135, ECO:0000269|PubMed:11389679, ECO:0000269|PubMed:11557028, ECO:0000269|PubMed:11564694, ECO:0000269|PubMed:11742812, ECO:0000269|PubMed:12117417, ECO:0000269|PubMed:12225859, ECO:0000269|PubMed:15769744, ECO:0000269|PubMed:16496379, ECO:0000269|PubMed:18262359, ECO:0000269|PubMed:25998567, ECO:0000269|PubMed:9751058}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Central carbon metabolism in cancer - Homo sapiens (human);Polythiazide Action Pathway;Methyclothiazide Action Pathway;Bumetanide Action Pathway;Spironolactone Action Pathway;Eplerenone Action Pathway;Triamterene Action Pathway;Amiloride Action Pathway;Leucine Stimulation on Insulin Signaling;Ethacrynic Acid Action Pathway;Quinethazone Action Pathway;Bendroflumethiazide Action Pathway;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;Aryl Hydrocarbon Receptor Pathway;Nuclear Receptors Meta-Pathway;mRNA, protein, and metabolite inducation pathway by cyclosporin A;Tryptophan catabolism;Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism;Metabolism of amino acids and derivatives;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;Valine, leucine and isoleucine degradation;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.251

Intolerance Scores

• loftool: 0.0798
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.147
• hipred: Y
• hipred_score: 0.765
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a5
• 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); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: amino acid transmembrane transport;cellular amino acid metabolic process;nervous system development;neutral amino acid transport;cell differentiation;leukocyte migration;L-alpha-amino acid transmembrane transport
• Cellular component: cytosol;plasma membrane;membrane;integral component of membrane;apical plasma membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;amino acid transmembrane transporter activity;neutral amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity;peptide antigen binding