SLC1A7

protein-coding

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

Gene summary

Enables glutamate:sodium symporter activity. Involved in neurotransmitter uptake. Predicted to be located in photoreceptor cell terminal bouton. Predicted to be active in glutamatergic synapse; postsynaptic membrane; and presynaptic membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006671.6

Inheritance

—

ClinVar variants

U:115B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr1:53,087,179-53,142,638

External References & Databases

Ensembl (ENSG00000162383)

Transcript & Mutation Effects

hg38 • Region Span ~55.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC1A7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 118

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006671.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			114 clinvar	5 clinvar		119
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	115	7	0	122

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006671.6	RefSeq	NP_006662.3	11	MANE Select
ENST00000371494.9	Ensembl	ENSP00000360549.5	11	MANE Select
NM_001287595.2	RefSeq	NP_001274524.1	11	Standard
NM_001287596.2	RefSeq	NP_001274525.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

neurotransmitter uptake
ion transport
dicarboxylic acid transport
glutamate secretion
L-glutamate transmembrane transport

Molecular Function

L-glutamate transmembrane transporter activity
high-affinity glutamate transmembrane transporter activity
amino acid transmembrane transporter activity

Cellular Component

plasma membrane
integral component of membrane
presynapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371494
Coding exons: 11
Length: 55435
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 71
Defined: 125748
p: 0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0738	358	362	0.989	0.0000238	3613
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00098	0.00098	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00057	0.00056	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.813
RVIS EVS: -0.44
RVIS percentile EVS: 24.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.311

Gene Damage Prediction

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