SLC38A10

protein-coding

solute carrier family 38 member 10, 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 act upstream of or within bone development. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001037984.3

Inheritance

—

ClinVar variants

U:133B:18

Top phenotype

SLC38A10-related disorder

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr17:81,244,811-81,295,547

External References & Databases

Ensembl (ENSG00000157637)

Transcript & Mutation Effects

hg38 • Region Span ~50.7 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 SLC38A10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 131

SLC38A10-related disorderTotal: 8

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001037984.3. 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			4 clinvar	3 clinvar	1 clinvar	8
missense			123 clinvar	14 clinvar		137
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	133	17	1	151

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 98 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001037984.3	RefSeq	NP_001033073.1	16	MANE Select
ENST00000374759.8	Ensembl	ENSP00000363891.3	16	MANE Select
NM_138570.4	RefSeq	NP_612637.1	14	Standard
ENST00000288439.10	Ensembl	ENSP00000288439.5	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

amino acid transmembrane transport
sodium ion transport
bone development

Molecular Function

amino acid transmembrane transporter activity

Cellular Component

Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374759
Coding exons: 16
Length: 50548
Individuals with no LoFs: 125647
Homozygous LoFs: 0
Heterozygous LoFs: 100
Defined: 125747
p: 0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.566	679	722	0.941	0.0000475	7176
Missense (PolyPhen)		195	232.86	0.83741		2380
Synonymous	-0.373	331	322	1.03	0.0000238	2381
Loss of Function	2.20	21	35.0	0.599	0.00000175	385

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00029	0.00025	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.00051	0.00049	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.00047	0.00045	rare
South Asian	0.00046	0.00042	rare
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Putative sodium-dependent amino acid/proton antiporter. {ECO:0000250}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

LoFtool: 0.802
RVIS EVS: 1.13
RVIS percentile EVS: 92.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.487

Gene Damage Prediction

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