SLC7A3

solute carrier family 7 member 3, the group of Solute carrier family 7

Basic information

Region (hg38): X:70925579-70931125

Links

ENSG00000165349 ∙ NCBI:84889 ∙ OMIM:300443 ∙ HGNC:11061 ∙ Uniprot:Q8WY07 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLC7A3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A3 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	1	10
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	9	1

Variants in SLC7A3

This is a list of pathogenic ClinVar variants found in the SLC7A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70925875-G-A		SLC7A3-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 08, 2022)
X-70925882-T-C			Likely benign (Mar 01, 2023)
X-70925907-C-G		SLC7A3-related disorder	Likely benign (Mar 01, 2024)
X-70925912-C-T			Likely benign (Jul 01, 2022)
X-70925927-G-A			Likely benign (Feb 01, 2023)
X-70926096-G-A		not specified	Uncertain significance (Aug 04, 2023)
X-70926576-A-G		SLC7A3-related disorder	Uncertain significance (Nov 15, 2022)
X-70926613-C-T		not specified	Uncertain significance (Jan 03, 2024)
X-70927322-G-C		not specified	Uncertain significance (May 06, 2024)
X-70927333-A-G		not specified	Uncertain significance (Jun 03, 2022)
X-70927535-T-C		not specified	Uncertain significance (Feb 14, 2023)
X-70927830-C-G			Uncertain significance (Jun 01, 2019)
X-70927836-A-G		SLC7A3-related disorder	Benign (Sep 30, 2019)
X-70927840-C-T		not specified	Uncertain significance (Jan 04, 2022)
X-70927864-A-C		not specified	Uncertain significance (Nov 18, 2023)
X-70927989-G-A		SLC7A3-related disorder	Likely benign (Feb 24, 2020)
X-70927996-C-T		not specified	Likely benign (Dec 20, 2021)
X-70928250-G-A		not specified	Uncertain significance (Nov 08, 2022)
X-70928520-G-A		SLC7A3-related disorder	Uncertain significance (Feb 24, 2023)
X-70928545-G-A			Likely benign (Apr 01, 2023)
X-70928550-T-C		not specified	Uncertain significance (Mar 07, 2024)
X-70928555-A-G		not specified	Uncertain significance (Dec 06, 2023)
X-70928588-A-G		not specified	Uncertain significance (Jul 05, 2023)
X-70928901-G-C		not specified	Uncertain significance (May 09, 2023)
X-70928912-A-G		not specified	Uncertain significance (Oct 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A3	protein_coding	protein_coding	ENST00000374299	11	5544

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00386	125640	0	1	125641	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	162	246	0.659	0.0000196	3934
Missense in Polyphen		17	54.584	0.31145		1117
Synonymous	-0.355	102	97.5	1.05	0.00000778	1341
Loss of Function	3.75	0	16.4	0.00	0.00000111	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the uptake of the cationic amino acids arginine, lysine and ornithine in a sodium-independent manner. {ECO:0000269|PubMed:11591158}.
• Pathway: 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: 0.151

Intolerance Scores

• loftool: 0.0426
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.463
• hipred: Y
• hipred_score: 0.537
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0456

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a3

Zebrafish Information Network

• Gene name: slc7a3a
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: amino acid transport;L-arginine import across plasma membrane;L-ornithine transmembrane transport;L-lysine transmembrane transport
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: L-ornithine transmembrane transporter activity;amino acid transmembrane transporter activity;arginine transmembrane transporter activity;L-lysine transmembrane transporter activity