SLC38A11

Summary

SLC38A11 (solute carrier family 38 member 11, HGNC:26836) is a protein-coding gene on chromosome 2q24.3, encoding Putative sodium-coupled neutral amino acid transporter 11 (Q08AI6). Putative sodium-dependent amino acid/proton antiporter.

Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport. Predicted to be active in membrane.

Source: NCBI Gene 151258 — RefSeq curated summary.

At a glance

• GWAS associations: 38
• Clinical variants (ClinVar): 77 total — 1 pathogenic
• MANE Select transcript: NM_001351537

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26836
Approved symbol	SLC38A11
Name	solute carrier family 38 member 11
Location	2q24.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39822, AVT2
Ensembl gene	ENSG00000169507
Ensembl biotype	protein_coding
OMIM	616526
Entrez	151258

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 6 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000303735, ENST00000409058, ENST00000409149, ENST00000409662, ENST00000424914, ENST00000465898, ENST00000470576, ENST00000483641, ENST00000492134, ENST00000493887, ENST00000685975

RefSeq mRNA: 6 — MANE Select: NM_001351537 NM_001199148, NM_001351537, NM_001351538, NM_001351539, NM_001351540, NM_173512

CCDS: CCDS2224, CCDS56142, CCDS92885

Canonical transcript exons

ENST00000685975 — 12 exons

Exon	Start	End
ENSE00001130083	164939450	164939556
ENSE00001130511	164911636	164911748
ENSE00001582244	164944569	164944634
ENSE00003478006	164954631	164954745
ENSE00003517409	164937350	164937429
ENSE00003531046	164945593	164945727
ENSE00003567881	164915112	164915273
ENSE00003628013	164915903	164915973
ENSE00003672515	164908640	164908771
ENSE00003928844	164955209	164955525
ENSE00003932117	164952707	164952781
ENSE00003934453	164894354	164898730

Expression profiles

Bgee: expression breadth ubiquitous, 185 present calls, max score 94.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7837 / max 90.9503, expressed in 177 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
31645	0.2395	100
31644	0.2213	99
31643	0.1263	41
31642	0.0798	38
31647	0.0592	23
31646	0.0577	29

Top tissues by expression

250 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	94.98	gold quality
gall bladder	UBERON:0002110	91.68	gold quality
pancreatic ductal cell	CL:0002079	91.22	gold quality
metanephros cortex	UBERON:0010533	89.60	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.82	gold quality
epithelial cell of pancreas	CL:0000083	85.95	silver quality
primary visual cortex	UBERON:0002436	85.80	gold quality
spleen	UBERON:0002106	81.86	gold quality
right frontal lobe	UBERON:0002810	81.20	gold quality
caput epididymis	UBERON:0004358	81.14	gold quality
body of stomach	UBERON:0001161	80.88	gold quality
endothelial cell	CL:0000115	79.83	silver quality
middle temporal gyrus	UBERON:0002771	79.70	gold quality
occipital lobe	UBERON:0002021	79.56	gold quality
stomach	UBERON:0000945	79.17	gold quality
putamen	UBERON:0001874	77.77	gold quality
prostate gland	UBERON:0002367	77.71	gold quality
anterior cingulate cortex	UBERON:0009835	76.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.96	gold quality
cauda epididymis	UBERON:0004360	76.90	gold quality
seminal vesicle	UBERON:0000998	76.74	gold quality
pigmented layer of retina	UBERON:0001782	76.47	gold quality
retina	UBERON:0000966	76.46	gold quality
adenohypophysis	UBERON:0002196	76.04	gold quality
caudate nucleus	UBERON:0001873	75.88	gold quality
body of pancreas	UBERON:0001150	75.75	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	75.74	gold quality
amygdala	UBERON:0001876	75.31	gold quality
rectum	UBERON:0001052	74.98	gold quality
Brodmann (1909) area 23	UBERON:0013554	74.98	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-8495	yes	531.86
E-HCAD-35	yes	8.29
E-ANND-3	yes	6.93
E-GEOD-125970	yes	5.13

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CLDN19, CLDN3

miRNA regulators (miRDB)

26 targeting SLC38A11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-145-5P	99.92	71.13	1836
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-4480	99.42	66.02	735
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-375-3P	97.91	65.12	483
HSA-MIR-3691-3P	97.90	65.97	791

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc38a11	ENSDARG00000040257
mus_musculus	Slc38a11	ENSMUSG00000061171
rattus_norvegicus	Slc38a11	ENSRNOG00000004966
drosophila_melanogaster	CG13743	FBGN0033368
caenorhabditis_elegans	slc-36.4	WBGENE00010421
caenorhabditis_elegans	Y18D10A.23	WBGENE00012487
caenorhabditis_elegans		WBGENE00012629
caenorhabditis_elegans		WBGENE00012804
caenorhabditis_elegans		WBGENE00019837
caenorhabditis_elegans		WBGENE00020837

Paralogs (15): SLC38A5 (ENSG00000017483), SLC32A1 (ENSG00000101438), SLC38A7 (ENSG00000103042), SLC38A1 (ENSG00000111371), SLC36A1 (ENSG00000123643), SLC38A2 (ENSG00000134294), SLC38A4 (ENSG00000139209), SLC38A6 (ENSG00000139974), SLC38A10 (ENSG00000157637), SLC38A8 (ENSG00000166558), SLC38A9 (ENSG00000177058), SLC36A4 (ENSG00000180773), SLC36A3 (ENSG00000186334), SLC36A2 (ENSG00000186335), SLC38A3 (ENSG00000188338)

Protein

Protein identifiers

Putative sodium-coupled neutral amino acid transporter 11 — Q08AI6 (reviewed: Q08AI6)

Alternative names: Solute carrier family 38 member 11

All UniProt accessions (4): A0A8I5QKK7, B8ZZ86, Q08AI6, H7C1P1

UniProt curated annotations — full annotation on UniProt →

Function. Putative sodium-dependent amino acid/proton antiporter.

Subcellular location. Membrane.

Similarity. Belongs to the amino acid/polyamine transporter 2 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q08AI6-1	1	yes
Q08AI6-2	2

RefSeq proteins (6): NP_001186077, NP_001338466, NP_001338467, NP_001338468, NP_001338469, NP_775783 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013057	AA_transpt_TM	Domain

Pfam: PF01490

UniProt features (16 total): transmembrane region 10, glycosylation site 2, chain 1, topological domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q08AI6-F1	88.50	0.74

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (2): 44, 275

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 71 (showing top): GOBP_AMINO_ACID_TRANSMEMBRANE_TRANSPORT, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_ORGANIC_ACID_TRANSPORT, chr2q24, GOBP_AMINO_ACID_TRANSPORT, GOBP_ORGANIC_ANION_TRANSPORT, HAND1E47_01, LINDVALL_IMMORTALIZED_BY_TERT_UP, GOBP_TRANSMEMBRANE_TRANSPORT, GOBP_SODIUM_ION_TRANSPORT, GOMF_L_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_AMINO_ACID_TRANSMEMBRANE_TRANSPORTER_ACTIVITY, GOMF_TRANSPORTER_ACTIVITY, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, RATTENBACHER_BOUND_BY_CELF1

GO Biological Process (5): amino acid transmembrane transport (GO:0003333), sodium ion transport (GO:0006814), monoatomic ion transport (GO:0006811), amino acid transport (GO:0006865), L-alpha-amino acid transmembrane transport (GO:1902475)

GO Molecular Function (2): L-amino acid transmembrane transporter activity (GO:0015179), protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
amino acid transport	1
transmembrane transport	1
metal ion transport	1
amino acid transmembrane transport	1
L-amino acid transport	1
carboxylic acid transmembrane transport	1
amino acid transmembrane transporter activity	1
carboxylic acid transmembrane transporter activity	1
L-alpha-amino acid transmembrane transport	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

543 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC38A11	REELD1	A0A1B0GV85	595
SLC38A11	SLC38A9	Q8NBW4	560
SLC38A11	C16orf96	A6NNT2	551
SLC38A11	ZNF142	P52746	460
SLC38A11	SLC7A4	O43246	452
SLC38A11	SLC43A2	Q8N370	433
SLC38A11	COBLL1	Q53SF7	419
SLC38A11	SLC6A15	Q9H2J7	381
SLC38A11	GLB1L	Q6UWU2	380
SLC38A11	CSRNP3	Q8WYN3	374
SLC38A11	KRTAP19-1	Q8IUB9	366
SLC38A11	GJD4	Q96KN9	364
SLC38A11	SLC3A1	Q07837	360
SLC38A11	SLC38A10	Q9HBR0	355
SLC38A11	SLC7A8	Q9UHI5	351

IntAct

4 interactions, top by confidence:

A	B	Type	Score
TUSC5	SLC38A11	psi-mi:“MI:0915”(physical association)	0.560
TUSC5	SLC38A11	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): TUSC5 (Two-hybrid), SLC38A11 (Affinity Capture-MS)

ESM2 similar proteins: A1YG32, A2VCW5, A2VE31, D3Z813, F4KBM7, G3UVW3, O80668, P38176, P39981, P40074, P40501, P47082, Q08AI6, Q0WQJ3, Q17598, Q19425, Q28HE5, Q28I47, Q3U1J0, Q3USY0, Q503G8, Q54S12, Q5E9S9, Q5EA97, Q5F468, Q5R443, Q5RE87, Q5SPB1, Q5XH90, Q610N4, Q6DEL1, Q6DFE7, Q6WWW3, Q8CFE6, Q8HXI3, Q8IZM9, Q8K2P7, Q8R1S9, Q8WUX1, Q969I6

Diamond homologs: A8KBL5, D3Z813, P39981, Q08AI6, Q3USY0, Q5EA97, Q5RE87, Q8HXI3, Q969I6, P38176, P40074, P40501

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	64
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1526927	GRCh37/hg19 2q24.2-24.3(chr2:163168812-167567296)	Pathogenic

SpliceAI

2222 predictions. Top by Δscore:

Variant	Effect	Δscore
2:164908632:GTAC:G	donor_loss	1.0000
2:164908633:TAC:T	donor_loss	1.0000
2:164908634:A:AC	donor_gain	1.0000
2:164908634:AC:A	donor_loss	1.0000
2:164908635:C:CC	donor_gain	1.0000
2:164908635:CTCA:C	donor_gain	1.0000
2:164908636:TCA:T	donor_loss	1.0000
2:164908637:C:CC	donor_loss	1.0000
2:164908638:A:AC	donor_gain	1.0000
2:164908638:A:C	donor_loss	1.0000
2:164908639:C:CC	donor_gain	1.0000
2:164908639:C:CG	donor_loss	1.0000
2:164908639:CA:C	donor_gain	1.0000
2:164908639:CATTG:C	donor_gain	1.0000
2:164915213:G:C	donor_gain	1.0000
2:164915894:AATAC:A	donor_loss	1.0000
2:164915895:ATACT:A	donor_loss	1.0000
2:164915896:TACTC:T	donor_loss	1.0000
2:164915897:AC:A	donor_loss	1.0000
2:164915898:C:CG	donor_loss	1.0000
2:164915899:T:TC	donor_loss	1.0000
2:164915900:CA:C	donor_loss	1.0000
2:164915901:A:C	donor_loss	1.0000
2:164915974:C:CC	acceptor_gain	1.0000
2:164937344:A:C	donor_gain	1.0000
2:164937344:ACTT:A	donor_loss	1.0000
2:164937345:CTT:C	donor_loss	1.0000
2:164937346:TTA:T	donor_loss	1.0000
2:164937348:A:AC	donor_gain	1.0000
2:164937348:ACATG:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000031962 (2:164905055 G>T), RS1000090344 (2:164956934 A>G), RS1000120145 (2:164956740 TGAC>T), RS1000173879 (2:164912361 T>C), RS1000321133 (2:164949556 T>A,C), RS1000325395 (2:164950606 G>T), RS1000373365 (2:164949774 G>C), RS1000380627 (2:164937401 G>A), RS1000438262 (2:164910874 C>T), RS1000494287 (2:164912330 T>A), RS1000568363 (2:164925578 A>G), RS1000599306 (2:164925877 C>G), RS1000751577 (2:164905370 G>A), RS1000758625 (2:164911975 T>C), RS1000812456 (2:164942384 A>G)

Disease associations

OMIM: gene MIM:616526 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

38 associations (top):

Study	Trait	p-value
GCST002579_8	Heschl’s gyrus morphology	2.000000e-06
GCST005950_14	Body mass index x sex x age interaction (4df test)	4.000000e-07
GCST005951_55	Body mass index	3.000000e-06
GCST005952_7	Body mass index (age>50)	4.000000e-09
GCST005956_34	Waist-to-hip ratio adjusted for BMI	2.000000e-13
GCST005957_2	Waist-to-hip ratio adjusted for BMI (age <50)	1.000000e-16
GCST005958_3	Waist-to-hip ratio adjusted for BMI (age >50)	1.000000e-16
GCST005962_14	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	1.000000e-29
GCST011687_2	Systolic blood pressure	6.000000e-07
GCST90020024_1152	A body shape index	2.000000e-12
GCST90020024_1153	A body shape index	2.000000e-11
GCST90020024_1154	A body shape index	7.000000e-09
GCST90020025_1719	Waist-to-hip ratio adjusted for BMI	4.000000e-14
GCST90020025_1724	Waist-to-hip ratio adjusted for BMI	1.000000e-21
GCST90020025_1725	Waist-to-hip ratio adjusted for BMI	2.000000e-19
GCST90020025_1726	Waist-to-hip ratio adjusted for BMI	4.000000e-15
GCST90020025_1727	Waist-to-hip ratio adjusted for BMI	5.000000e-08
GCST90020025_1728	Waist-to-hip ratio adjusted for BMI	7.000000e-10
GCST90020025_1729	Waist-to-hip ratio adjusted for BMI	1.000000e-11
GCST90020025_1730	Waist-to-hip ratio adjusted for BMI	1.000000e-09
GCST90020025_1731	Waist-to-hip ratio adjusted for BMI	1.000000e-10
GCST90020026_366	Hip index	3.000000e-10
GCST90020026_367	Hip index	5.000000e-09
GCST90020026_368	Hip index	1.000000e-09
GCST90020027_566	Waist-hip index	2.000000e-13
GCST90020027_571	Waist-hip index	1.000000e-21
GCST90020027_572	Waist-hip index	7.000000e-20
GCST90020027_573	Waist-hip index	7.000000e-15
GCST90020027_574	Waist-hip index	3.000000e-08
GCST90020027_575	Waist-hip index	4.000000e-08

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0006335	systolic blood pressure
EFO:0007789	BMI-adjusted waist circumference
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: transporter — Orphan SLC38 transporters

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation	4
Cyclosporine	decreases expression	3
Estradiol	decreases expression, affects expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Aflatoxin B1	affects expression, decreases expression	2
mivebresib	decreases expression	1
fluorene-9-bisphenol	increases expression	1
methyleugenol	decreases expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
2,6-dichloro-(1,4)benzoquinone	increases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Amiodarone	increases expression	1
Azathioprine	decreases expression	1
Quercetin	decreases expression	1
Silicon Dioxide	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4TE	HuH7-SLC38A11-KO-c4	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.