SLC1A7

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

Basic information

Region (hg38): 1:53087179-53142638

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.

• not_specified (100 variants)
• not_provided (1 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. These statistics are base on transcript: NM_000006671.6. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			96	3		99
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	5	0

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