SLC7A1

solute carrier family 7 member 1, the group of Solute carrier family 7

Basic information

Region (hg38): 13:29509413-29595688

Previous symbols: [ "ERR", "ATRC1" ]

Links

ENSG00000139514 ∙ NCBI:6541 ∙ OMIM:104615 ∙ HGNC:11057 ∙ Uniprot:P30825 ∙ 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 SLC7A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A1 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				1	5	6
missense			23	1	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	6

Variants in SLC7A1

This is a list of pathogenic ClinVar variants found in the SLC7A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-29514503-C-T		not specified	Uncertain significance (May 07, 2024)
13-29514539-C-A		not specified	Uncertain significance (Nov 27, 2023)
13-29516201-C-T		not specified	Uncertain significance (Dec 14, 2022)
13-29517200-C-T		not specified	Uncertain significance (Dec 12, 2023)
13-29517201-G-A			Benign (Oct 09, 2017)
13-29517256-G-T		not specified	Uncertain significance (Apr 06, 2022)
13-29517275-G-A		not specified	Uncertain significance (Nov 03, 2023)
13-29517284-C-A		not specified	Uncertain significance (Aug 15, 2023)
13-29517298-A-G		not specified	Uncertain significance (Apr 07, 2023)
13-29517299-T-C			Benign (Apr 20, 2018)
13-29519456-A-G		not specified	Uncertain significance (Mar 27, 2023)
13-29519488-G-C			Benign (Apr 20, 2018)
13-29522324-G-A			Benign (Oct 09, 2017)
13-29522370-T-C		not specified	Uncertain significance (Jun 24, 2022)
13-29523342-C-T		not specified	Uncertain significance (Jan 04, 2022)
13-29523389-G-A		not specified	Uncertain significance (Dec 14, 2023)
13-29523447-T-C		not specified	Uncertain significance (Feb 01, 2023)
13-29523453-C-T		not specified	Uncertain significance (Dec 02, 2022)
13-29524207-C-T		not specified	Uncertain significance (Oct 05, 2021)
13-29530542-T-C		not specified	Uncertain significance (Apr 18, 2023)
13-29530553-C-T		not specified	Likely benign (Dec 23, 2023)
13-29532832-A-G		not specified	Uncertain significance (Dec 12, 2023)
13-29532873-C-T			Benign (Apr 20, 2018)
13-29532921-G-A			Benign (Apr 20, 2018)
13-29532967-G-C		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A1	protein_coding	protein_coding	ENST00000380752	11	86279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00709	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.30	206	389	0.530	0.0000243	4055
Missense in Polyphen		67	193.82	0.34568		1957
Synonymous	0.190	167	170	0.981	0.0000124	1326
Loss of Function	4.12	2	23.6	0.0848	0.00000101	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: High-affinity, low capacity permease involved in the transport of the cationic amino acids (arginine, lysine and ornithine) in non-hepatic tissues. {ECO:0000269|PubMed:10485994}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);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;actions of nitric oxide in the heart;Lipoate metabolism;Valine, leucine and isoleucine degradation;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.305

Intolerance Scores

• loftool: 0.0567
• rvis_EVS: -1.22
• rvis_percentile_EVS: 5.6

Haploinsufficiency Scores

• pHI: 0.163
• hipred: Y
• hipred_score: 0.707
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.602

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a1
• Phenotype: growth/size/body region phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

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 plasma membrane;membrane;protein-containing complex
• Molecular function: L-ornithine transmembrane transporter activity;protein binding;amino acid transmembrane transporter activity;arginine transmembrane transporter activity;L-lysine transmembrane transporter activity