SLC7A6

solute carrier family 7 member 6, the group of Solute carrier family 7

Basic information

Region (hg38): 16:68264516-68301823

Links

ENSG00000103064 ∙ NCBI:9057 ∙ OMIM:605641 ∙ HGNC:11064 ∙ Uniprot:Q92536 ∙ 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 SLC7A6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A6 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		4
missense			18	1	3	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	19	5	3

Variants in SLC7A6

This is a list of pathogenic ClinVar variants found in the SLC7A6 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-68274758-C-T		not specified	Uncertain significance (Aug 04, 2022)
16-68274771-T-C		SLC7A6-related disorder	Likely benign (Apr 09, 2019)
16-68274804-A-T		SLC7A6-related disorder	Benign (Nov 11, 2019)
16-68274972-T-G		not specified	Uncertain significance (Dec 01, 2022)
16-68275155-C-T		SLC7A6-related disorder	Likely benign (Jun 19, 2019)
16-68275192-T-C		not specified	Uncertain significance (Nov 28, 2023)
16-68275226-G-A		not specified	Uncertain significance (May 17, 2023)
16-68287803-C-T		not specified	Uncertain significance (Dec 04, 2021)
16-68287814-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-68287833-T-C		not specified	Uncertain significance (Oct 22, 2021)
16-68290419-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-68290429-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-68291300-T-A			Benign (Apr 16, 2018)
16-68291575-G-A		SLC7A6-related disorder	Likely benign (Jun 18, 2019)
16-68291598-T-C		not specified	Uncertain significance (May 11, 2022)
16-68294740-C-T		not specified	Uncertain significance (Sep 09, 2021)
16-68294748-C-A		not specified	Uncertain significance (Apr 09, 2024)
16-68294787-G-C		not specified	Uncertain significance (Dec 20, 2022)
16-68296374-C-T		not specified	Uncertain significance (Jun 11, 2024)
16-68296494-A-G			Likely benign (Apr 10, 2018)
16-68296499-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-68296659-A-G		not specified	Uncertain significance (Feb 07, 2023)
16-68296727-T-C			Benign (Apr 16, 2018)
16-68296780-C-T		not specified	Uncertain significance (Feb 22, 2023)
16-68296805-T-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A6	protein_coding	protein_coding	ENST00000566454	9	37290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00973	0.988	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	229	294	0.780	0.0000167	3334
Missense in Polyphen		69	113.45	0.60821		1324
Synonymous	-0.898	134	121	1.10	0.00000743	1093
Loss of Function	2.70	7	20.1	0.349	8.63e-7	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00338	0.00338
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the sodium-independent uptake of dibasic amino acids and sodium-dependent uptake of some neutral amino acids. Requires coexpression with SLC3A2/4F2hc to mediate the uptake of arginine, leucine and glutamine. Also acts as an arginine/glutamine exchanger, following an antiport mechanism for amino acid transport, influencing arginine release in exchange for extracellular amino acids. Plays a role in nitric oxide synthesis in human umbilical vein endothelial cells (HUVECs) via transport of L-arginine. Involved in the transport of L-arginine in monocytes. Reduces uptake of ornithine in retinal pigment epithelial (RPE) cells. {ECO:0000269|PubMed:10903140, ECO:0000269|PubMed:11311135, ECO:0000269|PubMed:14603368, ECO:0000269|PubMed:15280038, ECO:0000269|PubMed:16785209, ECO:0000269|PubMed:17197568, ECO:0000269|PubMed:17329401, ECO:0000269|PubMed:9829974}.
• 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;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;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Amino acid transport across the plasma membrane;Amino acid and oligopeptide SLC transporters;Fibroblast growth factor-1;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.184
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.541
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a6

Gene ontology

• Biological process: amino acid transmembrane transport;cellular amino acid metabolic process;leukocyte migration;protein-containing complex assembly;L-alpha-amino acid transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;basolateral plasma membrane;intracellular membrane-bounded organelle
• Molecular function: amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity;antiporter activity