SLC38A7

protein-coding

solute carrier family 38 member 7, the group of Solute carrier family 38

Gene summary

Enables L-asparagine:sodium symporter activity and L-glutamine:sodium symporter activity. Involved in L-glutamine transport and asparagine transport. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_018231.3

Inheritance

—

ClinVar variants

U:53B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr16:58,665,109-58,684,770

External References & Databases

Ensembl (ENSG00000103042)

Transcript & Mutation Effects

hg38 • Region Span ~19.7 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 SLC38A7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 49

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018231.3. 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		2 clinvar	3
missense			51 clinvar		1 clinvar	52
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	0	3	56

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_018231.3	RefSeq	NP_060701.1	10	MANE Select
ENST00000219320.9	Ensembl	ENSP00000219320.3	10	MANE Select
NM_001308384.2	RefSeq	NP_001295313.1	7	Standard
NM_001369608.1	RefSeq	NP_001356537.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
sodium ion transport
asparagine transport
glutamine transport
branched-chain amino acid transport

Molecular Function

L-histidine transmembrane transporter activity
L-glutamate transmembrane transporter activity
protein binding
amino acid transmembrane transporter activity
L-amino acid transmembrane transporter activity

Cellular Component

integral component of membrane
axon
neuronal cell body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000570101
Coding exons: 10
Length: 19996
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.00	228	275	0.830	0.0000164	2961
Missense (PolyPhen)		86	115.02	0.74769		1243
Synonymous	0.399	113	119	0.953	0.00000803	964
Loss of Function	2.20	11	22.2	0.497	0.00000111	229

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000071	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates sodium-dependent transport of amino acids, preferentially L-glutamine. {ECO:0000250}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.504
RVIS EVS: -0.47
RVIS percentile EVS: 23.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.740

Gene Damage Prediction

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