SLC38A3

protein-coding

solute carrier family 38 member 3, the group of Solute carrier family 38

Gene summary

Enables L-amino acid transmembrane transporter activity. Involved in histidine transport and neutral amino acid transport. Located in plasma membrane. Implicated in developmental and epileptic encephalopathy 102. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_006841.6

Inheritance

ClinVar variants

P:7U:59B:6

Top phenotype

Developmental and epileptic encephalopathy 102

Max pathogenic AF

—

Genomic locus

chr3:50,205,246-50,221,486

External References & Databases

Ensembl (ENSG00000188338)

Transcript & Mutation Effects

hg38 • Region Span ~16.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

developmental and epileptic encephalopathy 102STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030881

Submitter: G2P

developmental and epileptic encephalopathy 102MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0030881

Submitter: Ambry Genetics

developmental and epileptic encephalopathy 102STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030881

Submitter: Labcorp Genetics (formerly Invitae)

developmental and epileptic encephalopathy 102STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0030881

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Developmental and epileptic encephalopathy 102AR

Manifestation: Neurologic; Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 34605855

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLC38A3 variants in ClinVar

5 Conditions Cataloged

Inborn genetic diseasesTotal: 54

Developmental and epileptic encephalopathy 102Total: 9

not specifiedTotal: 4

Short statureTotal: 3

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006841.6. 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	3 clinvar		4
missense	1 clinvar		58 clinvar	3 clinvar		62
nonsense	2 clinvar	1 clinvar				3
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)	2 clinvar					2
Total	6	1	59	6	0	72

Highest pathogenic variant AF is 0.000001373234

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 67 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006841.6	RefSeq	NP_006832.1	15	MANE Select
ENST00000614032.5	Ensembl	ENSP00000481301.1	15	MANE Select
ENST00000445096.5	Ensembl	ENSP00000480466.1	7	Standard
ENST00000610458.4	Ensembl	ENSP00000479737.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

GABAergic synapse - Homo sapiens (human)
Glutamatergic synapse - Homo sapiens (human)
Proximal tubule bicarbonate reclamation - Homo sapiens (human)
Amino acid transport across the plasma membrane
Amino acid and oligopeptide SLC transporters

Biological Process

amino acid transmembrane transport
sodium ion transport
amino acid transport
asparagine transport
glutamine transport

Molecular Function

L-histidine transmembrane transporter activity
amino acid transmembrane transporter activity
L-alanine transmembrane transporter activity
L-asparagine transmembrane transporter activity
L-glutamine transmembrane transporter activity

Cellular Component

plasma membrane
integral component of plasma membrane
basolateral plasma membrane

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sodium-dependent amino acid/proton antiporter. Mediates electrogenic cotransport of glutamine and sodium ions in exchange for protons. Also recognizes histidine, asparagine and alanine. May mediate amino acid transport in either direction under physiological conditions. May play a role in nitrogen metabolism and synaptic transmission. {ECO:0000250|UniProtKB:Q9JHZ9, ECO:0000269|PubMed:10823827}.;

Recessive Scores

pRec: 0.182

Essentials

Indispensability pred.: E
Indispensability score: 0.731