SLC38A11

protein-coding

solute carrier family 38 member 11, the group of Solute carrier family 38

Gene summary

Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001351537.2

Inheritance

—

ClinVar variants

U:70B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.18

Max pathogenic AF

—

Genomic locus

chr2:164,894,354-164,955,525

External References & Databases

Ensembl (ENSG00000169507)

Transcript & Mutation Effects

hg38 • Region Span ~61.2 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 SLC38A11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001351537.2. 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			66 clinvar	1 clinvar		67
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	70	2	0	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001351537.2	RefSeq	NP_001338466.1	12	MANE Select
ENST00000685975.1	Ensembl	ENSP00000508649.1	12	MANE Select
NM_001199148.2	RefSeq	NP_001186077.1	10	Standard
NM_001351538.2	RefSeq	NP_001338467.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
sodium ion transport

Molecular Function

amino acid transmembrane transporter activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409149
Coding exons: 10
Length: 59340
Individuals with no LoFs: 125656
Homozygous LoFs: 0
Heterozygous LoFs: 89
Defined: 125745
p: 0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0782	208	211	0.985	0.0000103	2642
Missense (PolyPhen)		71	73.137	0.97078		972
Synonymous	-0.334	80	76.3	1.05	0.00000400	812
Loss of Function	-0.697	20	16.9	1.18	7.96e-7	228

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.00065	0.00061	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00029	0.00027	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00045	0.00044	rare
South Asian	0.00025	0.00023	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000305}.;

Intolerance Scores

LoFtool: 0.793
RVIS EVS: 0.02
RVIS percentile EVS: 55.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0890

Gene Damage Prediction

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