SLC1A7

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

Basic information

Region (hg38): 1:53087178-53142638

Links

ENSG00000162383 ∙ NCBI:6512 ∙ OMIM:604471 ∙ HGNC:10945 ∙ Uniprot:O00341 ∙ 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 SLC1A7 gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC1A7 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	1	2
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	1

Variants in SLC1A7

This is a list of pathogenic ClinVar variants found in the SLC1A7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53088042-G-A			Likely benign (Feb 01, 2023)
1-53088050-G-A		not specified	Uncertain significance (Feb 05, 2024)
1-53088052-T-G		not specified	Uncertain significance (Jun 06, 2022)
1-53088187-T-G		not specified	Uncertain significance (Sep 27, 2021)
1-53088204-C-G		not specified	Uncertain significance (Jan 04, 2024)
1-53088894-G-A		not specified	Uncertain significance (May 15, 2023)
1-53089815-G-T		not specified	Uncertain significance (May 26, 2022)
1-53089852-C-T		not specified	Uncertain significance (May 04, 2022)
1-53089864-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-53090643-C-T		not specified	Uncertain significance (Oct 05, 2022)
1-53090709-T-G		not specified	Uncertain significance (Jan 29, 2024)
1-53090738-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-53090762-T-C		not specified	Uncertain significance (Feb 22, 2023)
1-53092597-C-G		not specified	Uncertain significance (Feb 27, 2023)
1-53092598-A-G			Benign (Jul 18, 2018)
1-53092599-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-53092635-A-C		not specified	Uncertain significance (Nov 17, 2022)
1-53092642-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-53092663-C-T		not specified	Uncertain significance (Mar 24, 2023)
1-53092709-C-A		not specified	Uncertain significance (Dec 26, 2023)
1-53092719-A-G		not specified	Uncertain significance (Sep 27, 2021)
1-53092732-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-53092787-C-G		not specified	Uncertain significance (Jul 13, 2021)
1-53093486-T-A		not specified	Uncertain significance (Nov 30, 2022)
1-53093491-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLC1A7	protein_coding	protein_coding	ENST00000371494	11	55435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.53e-11	0.139	125677	0	71	125748	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0738	358	362	0.989	0.0000238	3613
Missense in Polyphen		149	166.8	0.89329		1600
Synonymous	-0.240	166	162	1.02	0.0000121	1189
Loss of Function	0.515	17	19.5	0.874	8.29e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000479	0.000475
Ashkenazi Jewish	0.00	0.00
East Asian	0.000979	0.000979
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000979	0.000979
South Asian	0.000566	0.000555
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transports L-glutamate; the L-glutamate uptake is sodium- and voltage-dependent and chloride-independent. Its associated chloride conductance may participate in visual processing.
• Pathway: Glutamatergic synapse - Homo sapiens (human);Purine metabolism;Amino acid and oligopeptide SLC transporters;Transport of inorganic cations/anions and amino acids/oligopeptides;SLC-mediated transmembrane transport;Transport of small molecules;Neuronal System;Histidine metabolism;Glutamate Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.813
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.71

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.251
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.311

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc1a7

Gene ontology

• Biological process: neurotransmitter uptake;ion transport;dicarboxylic acid transport;glutamate secretion;L-glutamate transmembrane transport;neurotransmitter reuptake
• Cellular component: plasma membrane;integral component of membrane;presynapse
• Molecular function: L-glutamate transmembrane transporter activity;high-affinity glutamate transmembrane transporter activity;amino acid transmembrane transporter activity