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.

not_specified (42 variants)
SLC7A6-related_disorder (5 variants)
not_provided (3 variants)

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. These statistics are base on transcript: NM_000003983.6. 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				4 clinvar		4
missense			40 clinvar	3 clinvar	3 clinvar	46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	7	3

Loading clinvar variants...

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
Phenotype

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