SLC7A13

solute carrier family 7 member 13, the group of Solute carrier family 7

Basic information

Region (hg38): 8:86214063-86321146

Links

ENSG00000164893 ∙ NCBI:157724 ∙ OMIM:617256 ∙ HGNC:23092 ∙ Uniprot:Q8TCU3 ∙ 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 SLC7A13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC7A13 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				11	8	19
missense			50	7	9	66
nonsense			4			4
start loss			1			1
frameshift			2			2
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	0	0	57	19	18

Variants in SLC7A13

This is a list of pathogenic ClinVar variants found in the SLC7A13 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-86214405-TCCGACATC-T			Benign (Jan 30, 2024)
8-86214418-C-T			Benign (Jan 25, 2024)
8-86214456-T-C			Uncertain significance (Jan 07, 2024)
8-86214471-A-G			Benign (Jan 29, 2024)
8-86214514-G-T		not specified	Uncertain significance (Aug 02, 2021)
8-86214528-A-C			Uncertain significance (Nov 18, 2023)
8-86214529-A-G			Likely benign (Oct 13, 2023)
8-86214598-C-T		not specified	Uncertain significance (Oct 06, 2023)
8-86214611-G-A			Likely benign (Dec 19, 2023)
8-86214618-A-T		not specified	Uncertain significance (Jul 26, 2022)
8-86214620-TG-T			Uncertain significance (Jun 10, 2022)
8-86214637-A-G			Likely benign (Oct 03, 2023)
8-86214640-A-G			Likely benign (Apr 24, 2023)
8-86217473-A-G			Benign (Jan 30, 2024)
8-86217477-G-T			Benign (Dec 06, 2023)
8-86217487-G-A			Likely benign (Jun 01, 2021)
8-86217490-T-A		not specified	Uncertain significance (May 23, 2023)
8-86217494-T-A		not specified	Uncertain significance (Mar 18, 2024)
8-86217503-T-G		not specified	Uncertain significance (Jan 16, 2024)
8-86217507-C-T			Uncertain significance (Apr 27, 2023)
8-86217510-C-T			Benign (Jan 30, 2024)
8-86217551-C-T			Benign (Jan 25, 2024)
8-86217552-G-A		not specified	Uncertain significance (Dec 21, 2021)
8-86217567-T-C			Likely benign (Dec 15, 2023)
8-86217573-A-C		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC7A13	protein_coding	protein_coding	ENST00000297524	4	107095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.48e-13	0.00724	125706	0	29	125735	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.899	282	243	1.16	0.0000117	2985
Missense in Polyphen		72	64.237	1.1209		845
Synonymous	-0.705	103	94.3	1.09	0.00000472	994
Loss of Function	-0.688	18	15.1	1.19	7.94e-7	188

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000888	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000165	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mediates the transport L-aspartate and L-glutamate in a sodium-independent manner. {ECO:0000250}.

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.240
• rvis_EVS: 1.93
• rvis_percentile_EVS: 97.48

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.106

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc7a13
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: amino acid transmembrane transport;L-alpha-amino acid transmembrane transport
• Cellular component: integral component of membrane
• Molecular function: L-amino acid transmembrane transporter activity