SLC38A6

protein-coding

solute carrier family 38 member 6, the group of Solute carrier family 38

Gene summary

Predicted to enable L-glutamate transmembrane transporter activity and L-glutamine transmembrane transporter activity. Predicted to be involved in L-glutamine transport and amino acid transmembrane transport. Predicted to be located in membrane and synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_153811.3

Inheritance

—

ClinVar variants

U:58B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.07

Max pathogenic AF

—

Genomic locus

chr14:60,981,114-61,114,316

External References & Databases

Ensembl (ENSG00000139974)

Transcript & Mutation Effects

hg38 • Region Span ~133.2 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 SLC38A6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153811.3. 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		1
missense			54 clinvar	5 clinvar		59
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	58	6	0	64

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153811.3	RefSeq	NP_722518.2	16	MANE Select
ENST00000267488.9	Ensembl	ENSP00000267488.4	16	MANE Select
NM_001172702.2	RefSeq	NP_001166173.1	17	Standard
ENST00000354886.6	Ensembl	ENSP00000346959.2	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
sodium ion transport

Molecular Function

amino acid transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000354886
Coding exons: 17
Length: 102620
Individuals with no LoFs: 125594
Homozygous LoFs: 0
Heterozygous LoFs: 154
Defined: 125748
p: 0.000613

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.470	260	240	1.09	0.0000108	3342
Missense (PolyPhen)		83	87.044	0.95354		1226
Synonymous	-0.668	92	84.2	1.09	0.00000392	993
Loss of Function	-0.330	29	27.1	1.07	0.00000124	377

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00082	0.00080	rare
Latino/Admixed American	0.00053	0.00049	rare
Ashkenazi Jewish	0.0028	0.0028	notable
East Asian	0.0016	0.0015	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00042	0.00040	rare
South Asian	0.00057	0.00052	rare
Other	0.0011	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable sodium-dependent amino acid/proton antiporter, could be a neuronal transporter for glutamate. {ECO:0000250|UniProtKB:G3UVW3}.;

Recessive Scores

pRec: 0.287

Intolerance Scores

LoFtool: 0.988
RVIS EVS: -0.49
RVIS percentile EVS: 22.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0354

Gene Damage Prediction

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