SLC7A2

solute carrier family 7 member 2, the group of Solute carrier family 7

Basic information

Region (hg38): 8:17497088-17570573

Previous symbols: [ "ATRC2" ]

Links

ENSG00000003989 ∙ NCBI:6542 ∙ OMIM:601872 ∙ HGNC:11060 ∙ Uniprot:P52569 ∙ 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 SLC7A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A2 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					5	5
missense			46	3	5	54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	46	3	12

Variants in SLC7A2

This is a list of pathogenic ClinVar variants found in the SLC7A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-17538841-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-17538855-G-T		not specified	Uncertain significance (Nov 09, 2024)
8-17538864-A-G		not specified	Uncertain significance (Aug 12, 2021)
8-17538871-G-A		SLC7A2-related disorder	Benign (Nov 01, 2019)
8-17538903-T-G		not specified	Uncertain significance (Oct 12, 2024)
8-17538906-G-C		SLC7A2-related disorder	Benign (Nov 01, 2019)
8-17538911-C-A		not specified	Uncertain significance (Dec 02, 2024)
8-17538930-T-TC		SLC7A2-related disorder	Benign (Nov 26, 2019)
8-17538932-A-C		SLC7A2-related disorder	Benign (Nov 26, 2019)
8-17543321-G-A		SLC7A2-related disorder	Benign (Dec 06, 2019)
8-17543326-C-T		not specified	Uncertain significance (Sep 26, 2024)
8-17543329-C-T		not specified	Uncertain significance (May 02, 2023)
8-17543331-G-C		not specified	Uncertain significance (Dec 08, 2023)
8-17543334-G-A		not specified	Uncertain significance (May 18, 2023)
8-17543352-A-G		not specified	Uncertain significance (May 26, 2024)
8-17543448-A-G		not specified	Uncertain significance (Jan 03, 2024)
8-17543533-G-A		not specified	Uncertain significance (Sep 26, 2024)
8-17543544-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-17543571-G-T		not specified	Uncertain significance (Jan 17, 2024)
8-17543614-G-A		not specified	Uncertain significance (Jun 02, 2023)
8-17543644-A-G		not specified	Uncertain significance (Jan 04, 2024)
8-17543652-G-C		SLC7A2-related disorder	Benign (Dec 11, 2019)
8-17543661-G-A		not specified	Uncertain significance (May 29, 2024)
8-17543707-A-G		not specified	Uncertain significance (Sep 08, 2024)
8-17544468-A-G		not specified	Uncertain significance (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A2	protein_coding	protein_coding	ENST00000004531	12	73486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-11	0.660	125701	0	46	125747	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.41	477	398	1.20	0.0000219	4514
Missense in Polyphen		142	140.59	1.01		1584
Synonymous	-1.96	195	163	1.20	0.0000109	1426
Loss of Function	1.50	21	29.8	0.704	0.00000140	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000800	0.000794
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000220	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.000220	0.000217
South Asian	0.0000654	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine); the affinity for its substrates differs between isoforms created by alternative splicing. Isoform 1 functions as permease that mediates the transport of the cationic amino acids (arginine, lysine and ornithine), and it has much higher affinity for arginine than isoform 2. Isoform 2 functions as low-affinity, high capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) (PubMed:9174363). May play a role in classical or alternative activation of macrophages via its role in arginine transport. {ECO:0000250|UniProtKB:P18581, ECO:0000269|PubMed:9174363}.
• Pathway: Lysine Degradation;Hyperlysinemia I, Familial;2-aminoadipic 2-oxoadipic aciduria;Pyridoxine dependency with seizures;Saccharopinuria/Hyperlysinemia II;Glutaric Aciduria Type I;Hyperlysinemia II or Saccharopinuria;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;Valine, leucine and isoleucine degradation;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.0207
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.54

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.216
• ghis: 0.437

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.333

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a2
• Phenotype: immune system phenotype

Gene ontology

• Biological process: nitric oxide production involved in inflammatory response;cellular amino acid metabolic process;nitric oxide biosynthetic process;amino acid transport;macrophage activation;regulation of macrophage activation;regulation of inflammatory response;L-arginine import across plasma membrane;L-ornithine transmembrane transport;L-lysine transmembrane transport
• Cellular component: plasma membrane;integral component of plasma membrane;membrane;cell junction
• Molecular function: L-ornithine transmembrane transporter activity;amino acid transmembrane transporter activity;basic amino acid transmembrane transporter activity;arginine transmembrane transporter activity;L-lysine transmembrane transporter activity;L-arginine transmembrane transporter activity