SLC7A9

solute carrier family 7 member 9, the group of Solute carrier family 7

Basic information

Region (hg38): 19:32830509-32869767

Previous symbols: [ "CSNU3" ]

Links

ENSG00000021488 ∙ NCBI:11136 ∙ OMIM:604144 ∙ HGNC:11067 ∙ Uniprot:P82251 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cystinuria (Definitive), mode of inheritance: AR
• cystinuria type B (Supportive), mode of inheritance: Semidominant
• cystinuria (Strong), mode of inheritance: AR
• cystinuria (Strong), mode of inheritance: AD
• cystinuria (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cystinuria	AD/AR	Biochemical; Renal	Measures to maintain high fluid intake, as well as medical therapy (eg, urine alkalinization, and, in some, penicillamine) can be beneficial	Biochemical; Renal	5925065; 2502678; 10471498; 11157794; 12239244; 12371955; 12820697; 12820697; 17539912

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A9 gene.

• not provided (18 variants)
• Cystinuria (11 variants)
• Cystine urolithiasis (1 variants)
• SLC7A9-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A9 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		2	7	39	7	55
missense	6	6	61	4	2	79
nonsense	6	4				10
start loss						0
frameshift	8	5	2			15
inframe indel		1	2			3
splice donor/acceptor (+/-2bp)	4	3				7
splice region	1		6	4	1	12
non coding			8	23	49	80
Total	24	21	80	66	58

Highest pathogenic variant AF is 0.000131

Variants in SLC7A9

This is a list of pathogenic ClinVar variants found in the SLC7A9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-32830538-G-A		Cystinuria	Uncertain significance (Jan 13, 2018)
19-32830541-A-G		Cystinuria	Benign (Jan 11, 2020)
19-32830543-A-G		Cystinuria	Uncertain significance (Jan 13, 2018)
19-32830600-G-A		Cystinuria	Uncertain significance (Jan 13, 2018)
19-32830611-C-T		SLC7A9-related disorder	Benign (Nov 06, 2019)
19-32830612-G-A		Cystinuria • SLC7A9-related disorder	Uncertain significance (Apr 27, 2017)
19-32830638-C-G			Likely benign (Jan 19, 2024)
19-32830638-C-T		Cystinuria	Conflicting classifications of pathogenicity (Dec 26, 2023)
19-32830639-G-A			Pathogenic (Dec 11, 2023)
19-32830640-G-A		not specified • SLC7A9-related disorder	Benign (Jan 15, 2024)
19-32830652-C-CCATT			Uncertain significance (Jul 10, 2015)
19-32830680-C-T		Cystinuria	Conflicting classifications of pathogenicity (Nov 13, 2023)
19-32830681-G-A		Cystinuria	Benign/Likely benign (Jan 19, 2024)
19-32830682-G-A			Uncertain significance (Dec 24, 2021)
19-32830686-T-C		Cystinuria	Pathogenic (Jan 26, 2022)
19-32830811-A-G			Benign (Dec 08, 2019)
19-32830811-A-AGG			Benign (Aug 20, 2019)
19-32830869-C-G			Benign (Dec 08, 2019)
19-32833074-G-T			Benign (May 16, 2021)
19-32833141-GTACT-G		Cystinuria	Conflicting classifications of pathogenicity (Oct 03, 2023)
19-32833144-C-G		Cystine urolithiasis • Cystinuria	Likely pathogenic (Aug 26, 2024)
19-32833146-T-TA		Cystine urolithiasis	Pathogenic (Nov 23, 2022)
19-32833149-T-C		Cystinuria	Uncertain significance (Jan 12, 2018)
19-32833151-G-T		Cystinuria	Pathogenic (Feb 01, 2020)
19-32833160-T-C		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A9	protein_coding	protein_coding	ENST00000023064	12	39258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.06e-10	0.488	125624	0	124	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.805	256	295	0.868	0.0000189	3145
Missense in Polyphen		89	115.29	0.77196		1239
Synonymous	0.158	125	127	0.982	0.00000995	998
Loss of Function	1.12	17	22.8	0.747	9.83e-7	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000536	0.000535
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000704	0.000703
Middle Eastern	0.000489	0.000489
South Asian	0.000359	0.000359
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the high-affinity, sodium-independent transport of cystine and neutral and dibasic amino acids (system b(0,+)-like activity). Thought to be responsible for the high- affinity reabsorption of cystine in the kidney tubule. {ECO:0000269|PubMed:10471498, ECO:0000269|PubMed:10588648, ECO:0000269|PubMed:16609684}.
• Pathway: Protein digestion and absorption - Homo sapiens (human);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;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;Glycerophospholipid metabolism;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.273

Intolerance Scores

• loftool: 0.194
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.86

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.653
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a9
• Phenotype: homeostasis/metabolism phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: amino acid transmembrane transport;neutral amino acid transport;L-cystine transport;leukocyte migration;protein-containing complex assembly;L-alpha-amino acid transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;apical plasma membrane;brush border membrane
• Molecular function: protein binding;neutral amino acid transmembrane transporter activity;L-amino acid transmembrane transporter activity;L-cystine transmembrane transporter activity;peptide antigen binding