SLC7A1

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

Basic information

Region (hg38): 13:29509414-29595688

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.

not_specified (49 variants)
not_provided (7 variants)

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. These statistics are base on transcript: NM_000003045.5. 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				2 clinvar	5 clinvar	7
missense			46 clinvar	2 clinvar	1 clinvar	49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	4	6

Loading clinvar variants...

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