SLC7A11

solute carrier family 7 member 11, the group of Solute carrier family 7

Basic information

Region (hg38): 4:138164097-138242349

Links

ENSG00000151012 ∙ NCBI:23657 ∙ OMIM:607933 ∙ HGNC:11059 ∙ Uniprot:Q9UPY5 ∙ 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 SLC7A11 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A11 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						0
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	0

Variants in SLC7A11

This is a list of pathogenic ClinVar variants found in the SLC7A11 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-138179253-A-G		not specified	Uncertain significance (Sep 17, 2021)
4-138179273-G-A		not specified	Uncertain significance (Jun 22, 2023)
4-138179295-T-G		not specified	Uncertain significance (Jul 27, 2022)
4-138179298-C-T		not specified	Likely benign (Mar 22, 2023)
4-138179342-G-A		not specified	Uncertain significance (Mar 17, 2023)
4-138180675-C-T		not specified	Uncertain significance (Nov 21, 2022)
4-138180715-G-A		not specified	Uncertain significance (Mar 24, 2023)
4-138180774-A-G		not specified	Uncertain significance (Sep 17, 2021)
4-138182308-C-T		not specified	Uncertain significance (Oct 26, 2022)
4-138182350-G-A		not specified	Uncertain significance (Jul 06, 2021)
4-138183265-A-G		not specified	Uncertain significance (Aug 30, 2021)
4-138185167-G-A		not specified	Uncertain significance (May 31, 2023)
4-138185201-T-C		not specified	Likely benign (Jul 12, 2023)
4-138185237-G-A		not specified	Uncertain significance (Apr 24, 2024)
4-138219347-T-C		not specified	Uncertain significance (Nov 17, 2022)
4-138223282-G-A		not specified	Uncertain significance (Oct 10, 2023)
4-138223292-T-G		not specified	Uncertain significance (May 14, 2024)
4-138223297-C-T		not specified	Uncertain significance (Jun 07, 2024)
4-138232285-T-C		not specified	Uncertain significance (Sep 13, 2023)
4-138232288-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-138232300-G-A		not specified	Uncertain significance (Aug 13, 2021)
4-138232327-A-G		not specified	Uncertain significance (May 04, 2023)
4-138232339-T-G		not specified	Uncertain significance (May 14, 2024)
4-138232344-C-T		not specified	Uncertain significance (Oct 18, 2021)
4-138232345-G-A		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A11	protein_coding	protein_coding	ENST00000280612	12	78253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000568	0.994	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	242	279	0.869	0.0000144	3215
Missense in Polyphen		92	115.04	0.79975		1382
Synonymous	-0.131	107	105	1.02	0.00000573	1046
Loss of Function	2.45	11	23.9	0.460	0.00000124	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000200	0.000200
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000198	0.000193
Middle Eastern	0.0000546	0.0000544
South Asian	0.000229	0.000229
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sodium-independent, high-affinity exchange of anionic amino acids with high specificity for anionic form of cystine and glutamate. {ECO:0000269|PubMed:15151999}.
• Pathway: Ferroptosis - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Nuclear Receptors Meta-Pathway;NRF2 pathway;Transcriptional activation by NRF2;mRNA, protein, and metabolite inducation pathway by cyclosporin A;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;Methionine and cysteine metabolism;Cell surface interactions at the vascular wall;Hemostasis;Basigin interactions (Consensus)

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.230
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.212
• hipred: N
• hipred_score: 0.393
• ghis: 0.445

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.677

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a11
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; neoplasm; pigmentation phenotype; vision/eye phenotype; immune system phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: amino acid transmembrane transport;glutathione metabolic process;visual learning;response to toxic substance;response to organic cyclic compound;ventricular system development;striatum development;adult behavior;regulation of neutrophil apoptotic process;cellular response to oxidative stress;glutathione transmembrane transport;response to nicotine;regulation of cell population proliferation;regulation of melanin biosynthetic process;lung alveolus development;modulation of chemical synaptic transmission;leukocyte migration;regulation of protein transport;response to redox state;limb development;lens fiber cell differentiation;platelet aggregation;glutamate homeostasis;L-glutamate import across plasma membrane;dipeptide import across plasma membrane;regulation of cysteine metabolic process;negative regulation of oxidative stress-induced neuron death;regulation of glutathione biosynthetic process;regulation of AMPA glutamate receptor clustering;regulation of glutamate metabolic process
• Cellular component: rough endoplasmic reticulum;cytoskeleton;plasma membrane;cell surface;integral component of membrane;brush border membrane;astrocyte projection
• Molecular function: protein binding;L-amino acid transmembrane transporter activity;cystine:glutamate antiporter activity