SLC22A31

Summary

SLC22A31 (solute carrier family 22 member 31, HGNC:27091) is a protein-coding gene on chromosome 16q24.3, encoding Putative solute carrier family 22 member 31 (A6NKX4). Organic anion transporter that mediates the uptake of ions.

Predicted to enable transmembrane transporter activity. Predicted to be involved in monoatomic ion transport and transmembrane transport. Predicted to be located in membrane.

Source: NCBI Gene 146429 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 107 total — 4 pathogenic
• MANE Select transcript: NM_001384763

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27091
Approved symbol	SLC22A31
Name	solute carrier family 22 member 31
Location	16q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000259803
Ensembl biotype	protein_coding
Entrez	146429

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 retained_intron, 3 protein_coding

ENST00000562855, ENST00000562916, ENST00000563595, ENST00000568161, ENST00000603735, ENST00000614943, ENST00000682282

RefSeq mRNA: 13 — MANE Select: NM_001384763 NM_001366322, NM_001384763, NM_001384764, NM_001384765, NM_001384766, NM_001384767, NM_001384768, NM_001384769, NM_001384770, NM_001384771, NM_001384772, NM_001384773, NM_001384775

CCDS: CCDS73927, CCDS92209

Canonical transcript exons

ENST00000682282 — 9 exons

Exon	Start	End
ENSE00002595071	89198652	89198797
ENSE00003471027	89198442	89198550
ENSE00003477767	89198122	89198336
ENSE00003552306	89195761	89196305
ENSE00003558808	89197298	89197409
ENSE00003917320	89200478	89200537
ENSE00003919340	89199023	89199191
ENSE00003919886	89199713	89199816
ENSE00003921080	89199413	89199567

Expression profiles

Bgee: expression breadth ubiquitous, 155 present calls, max score 97.60.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9835 / max 166.0564, expressed in 519 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
158614	1.8721	504
158613	0.1114	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	97.60	gold quality
cerebellar cortex	UBERON:0002129	97.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.20	gold quality
cerebellum	UBERON:0002037	96.16	gold quality
upper lobe of left lung	UBERON:0008952	92.36	gold quality
upper lobe of lung	UBERON:0008948	91.57	gold quality
right lung	UBERON:0002167	90.07	gold quality
pancreatic ductal cell	CL:0002079	89.70	silver quality
buccal mucosa cell	CL:0002336	84.76	gold quality
lung	UBERON:0002048	82.47	gold quality
body of pancreas	UBERON:0001150	81.42	gold quality
tendon of biceps brachii	UBERON:0008188	79.58	silver quality
lower lobe of lung	UBERON:0008949	79.42	silver quality
sperm	CL:0000019	77.31	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.36	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	76.25	silver quality
upper arm skin	UBERON:0004263	75.98	gold quality
right ovary	UBERON:0002118	75.89	gold quality
right testis	UBERON:0004534	75.30	gold quality
left testis	UBERON:0004533	75.24	gold quality
spleen	UBERON:0002106	73.82	gold quality
testis	UBERON:0000473	73.30	gold quality
left ovary	UBERON:0002119	73.14	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.09	gold quality
bone marrow	UBERON:0002371	72.98	gold quality
epithelial cell of pancreas	CL:0000083	72.32	gold quality
parotid gland	UBERON:0001831	72.04	gold quality
endothelial cell	CL:0000115	71.79	gold quality
ovary	UBERON:0000992	69.57	gold quality
cerebellar vermis	UBERON:0004720	69.47	silver quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	75.29
E-ANND-3	yes	21.25

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting SLC22A31, 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-4455	100.00	65.48	1587
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-7155-5P	98.65	66.14	1290
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-346	97.01	66.97	662

Cross-species orthologs

41 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc22a31	ENSDARG00000078882
drosophila_melanogaster	Orct	FBGN0019952
drosophila_melanogaster	CG15221	FBGN0030331
drosophila_melanogaster	Balat	FBGN0033778
drosophila_melanogaster	CG5592	FBGN0035645
drosophila_melanogaster	CG10486	FBGN0035647
drosophila_melanogaster	CG14691	FBGN0037829
drosophila_melanogaster	CG14855	FBGN0038260
drosophila_melanogaster	CG14856	FBGN0038261
drosophila_melanogaster	CG14857	FBGN0038262
drosophila_melanogaster	CG12783	FBGN0038448
drosophila_melanogaster	CG7333	FBGN0038715
drosophila_melanogaster	CG7342	FBGN0038716
drosophila_melanogaster	CG17751	FBGN0038717
drosophila_melanogaster	CG17752	FBGN0038718
drosophila_melanogaster	CG16727	FBGN0038719
drosophila_melanogaster	CG6231	FBGN0038720
drosophila_melanogaster	CG4465	FBGN0038750
drosophila_melanogaster	CG4462	FBGN0038752
drosophila_melanogaster	CG4459	FBGN0038753
drosophila_melanogaster	CG6356	FBGN0039178
drosophila_melanogaster	CG3690	FBGN0040350
drosophila_melanogaster	CG31103	FBGN0051103
drosophila_melanogaster	CG31106	FBGN0051106
drosophila_melanogaster	CG31272	FBGN0051272
drosophila_melanogaster	CG33233	FBGN0053233
drosophila_melanogaster	CG33234	FBGN0053234
drosophila_melanogaster	Orct2	FBGN0086365
drosophila_melanogaster	CG42269	FBGN0259164
drosophila_melanogaster	CG44098	FBGN0264907
caenorhabditis_elegans		WBGENE00003837
caenorhabditis_elegans	oct-1	WBGENE00003842
caenorhabditis_elegans		WBGENE00003843
caenorhabditis_elegans		WBGENE00006220
caenorhabditis_elegans		WBGENE00008110
caenorhabditis_elegans		WBGENE00011456
caenorhabditis_elegans		WBGENE00014127
caenorhabditis_elegans		WBGENE00017751
caenorhabditis_elegans		WBGENE00019408
caenorhabditis_elegans		WBGENE00020701
caenorhabditis_elegans		WBGENE00044455

Paralogs (22): SLC22A16 (ENSG00000004809), SLC22A17 (ENSG00000092096), SLC22A2 (ENSG00000112499), SLC22A7 (ENSG00000137204), SLC22A23 (ENSG00000137266), SLC22A14 (ENSG00000144671), SLC22A3 (ENSG00000146477), SLC22A8 (ENSG00000149452), SLC22A9 (ENSG00000149742), SVOPL (ENSG00000157703), SLC22A15 (ENSG00000163393), SVOP (ENSG00000166111), SLC22A11 (ENSG00000168065), SLC22A13 (ENSG00000172940), SLC22A1 (ENSG00000175003), SLC22A10 (ENSG00000184999), SLC22A25 (ENSG00000196600), SLC22A4 (ENSG00000197208), SLC22A5 (ENSG00000197375), SLC22A24 (ENSG00000197658), SLC22A12 (ENSG00000197891), SLC22A6 (ENSG00000197901)

Protein

Protein identifiers

Putative solute carrier family 22 member 31 — A6NKX4 (reviewed: A6NKX4)

All UniProt accessions (2): A0A087WY01, A6NKX4

UniProt curated annotations — full annotation on UniProt →

Function. Organic anion transporter that mediates the uptake of ions.

Subcellular location. Membrane.

Similarity. Belongs to the major facilitator (TC 2.A.1) superfamily. Organic cation transporter (TC 2.A.1.19) family.

Isoforms (2)

UniProt ID	Names	Canonical?
A6NKX4-1	1	yes
A6NKX4-2	2

RefSeq proteins (13): NP_001353251, NP_001371692, NP_001371693, NP_001371694, NP_001371695, NP_001371696, NP_001371697, NP_001371698, NP_001371699, NP_001371700, NP_001371701, NP_001371702, NP_001371704 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005828	MFS_sugar_transport-like	Family
IPR020846	MFS_dom	Domain
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF00083

UniProt features (28 total): topological domain 13, transmembrane region 12, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NKX4-F1	78.02	0.40

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): GOBP_TRANSMEMBRANE_TRANSPORT, LIU_LIVER_CANCER, GOMF_TRANSPORTER_ACTIVITY, KAT2A_TARGET_GENES, PCGF1_TARGET_GENES, SALL4_TARGET_GENES, SNAI1_TARGET_GENES, SUPT16H_TARGET_GENES, DESCARTES_MAIN_FETAL_SATELLITE_CELLS, ZBED5_TARGET_GENES, PRDM4_TARGET_GENES, TRAVAGLINI_LUNG_ALVEOLAR_EPITHELIAL_TYPE_2_CELL, TRAVAGLINI_LUNG_SIGNALING_ALVEOLAR_EPITHELIAL_TYPE_2_CELL, GOBP_MONOATOMIC_ION_TRANSPORT, GAVISH_3CA_MALIGNANT_METAPROGRAM_31_ALVEOLAR

GO Biological Process (2): monoatomic ion transport (GO:0006811), transmembrane transport (GO:0055085)

GO Molecular Function (1): transmembrane transporter activity (GO:0022857)

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
cellular process	1
transporter activity	1
transmembrane transport	1
cellular anatomical structure	1

Protein interactions and networks

STRING

426 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC22A31	SLC67A1	Q96BI1	671
SLC22A31	SLC22A25	Q6T423	624
SLC22A31	OR1L3	Q8NH93	506
SLC22A31	ZNF778	Q96MU6	506
SLC22A31	OR1L1	Q8NH94	483
SLC22A31	SLC35G4	P0C7Q5	478
SLC22A31	TRAPPC2L	Q9UL33	438
SLC22A31	C1orf105	O95561	437
SLC22A31	CCDC160	A6NGH7	432
SLC22A31	DCAF8L1	A6NGE4	430
SLC22A31	SLC35G3	Q8N808	418
SLC22A31	ERFE	Q4G0M1	416
SLC22A31	CPNE7	Q9UBL6	414
SLC22A31	ZNF280A	P59817	400
SLC22A31	ACSF3	Q4G176	390

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6NGC4, A6NKX4, A6NM10, F1NZP5, O96011, P0C242, P27544, P27545, Q0VCY6, Q2TBI8, Q3SYU3, Q4V8E5, Q5F2F2, Q5JZQ7, Q5RFI0, Q5U2T1, Q5U419, Q6AYM9, Q6GQT6, Q6PIS1, Q6TCG5, Q6UXD7, Q6UXT9, Q71RH2, Q7TNV1, Q7Z403, Q80ZE4, Q863Y8, Q86WI3, Q8BMT9, Q8CHK3, Q8IU68, Q8IXF9, Q8N9H8, Q8TBR7, Q8VC26, Q8WUG5, Q96N66, Q99640, Q99JT6

Diamond homologs: A1A5C7, A6NKX4, Q3SZQ2, Q3UHH2, Q8WUG5, Q9D9E0, Q9P290, Q9QZG1, A7MBE0, C0SPB2, Q0WUU6, Q3YAW7, Q46909, Q5RC45, Q5RLM2, Q96S37, Q9Y226, O02713, O75751, O77504, O88446, Q9VCA2, Q9WTW5, A0A0B5EMG9, A0A0D2YFZ8, A0A1D8PCL1, B2CPI7, J9VXV2, O08966, O23492, O52733, O74713, P0AE24, P0AE25, P11166, P11167, P12336, P13355, P14142, P14246

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	0
Uncertain significance	87
Likely benign	6
Benign	4

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
267474	Single allele	Pathogenic
267478	Single allele	Pathogenic
267480	Single allele	Pathogenic
3024606	GRCh37/hg19 16q24.2-24.3(chr16:87866576-89424113)x1	Pathogenic

SpliceAI

1227 predictions. Top by Δscore:

Variant	Effect	Δscore
16:89197293:CTCAC:C	donor_loss	1.0000
16:89197294:TCA:T	donor_loss	1.0000
16:89197295:CACC:C	donor_loss	1.0000
16:89197297:CCTGA:C	donor_gain	1.0000
16:89197405:CAGAT:C	acceptor_gain	1.0000
16:89197408:ATC:A	acceptor_loss	1.0000
16:89197410:C:CC	acceptor_gain	1.0000
16:89197410:C:CG	acceptor_loss	1.0000
16:89197411:T:C	acceptor_loss	1.0000
16:89198121:CA:C	donor_gain	1.0000
16:89198332:CCAGC:C	acceptor_gain	1.0000
16:89198333:CAGCC:C	acceptor_gain	1.0000
16:89198430:T:TA	donor_gain	1.0000
16:89198440:A:AC	donor_gain	1.0000
16:89198441:C:CC	donor_gain	1.0000
16:89198441:CGAG:C	donor_gain	1.0000
16:89198558:C:CT	acceptor_gain	1.0000
16:89199411:A:AC	donor_gain	1.0000
16:89199411:ACGAG:A	donor_gain	1.0000
16:89199412:C:CC	donor_gain	1.0000
16:89199412:CGAGC:C	donor_gain	1.0000
16:89197296:A:AC	donor_gain	0.9900
16:89197297:C:CC	donor_gain	0.9900
16:89197299:TGATC:T	donor_gain	0.9900
16:89197372:C:T	acceptor_gain	0.9900
16:89197406:AGAT:A	acceptor_gain	0.9900
16:89197407:GAT:G	acceptor_gain	0.9900
16:89197408:AT:A	acceptor_gain	0.9900
16:89198035:C:A	donor_gain	0.9900
16:89198097:ATGG:A	donor_gain	0.9900

AlphaMissense

2763 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000041781 (16:89201760 G>C), RS1000523714 (16:89196137 C>T), RS1000653062 (16:89198953 C>G,T), RS1000749275 (16:89200455 G>A,C), RS1000800276 (16:89200275 C>A), RS1000997397 (16:89196301 C>G,T), RS1001170723 (16:89202072 G>A), RS1001239970 (16:89198788 G>A), RS1001419751 (16:89198609 C>T), RS1001488172 (16:89198380 C>G), RS1001619281 (16:89203640 G>A), RS1001621855 (16:89201975 C>T), RS1002476310 (16:89199297 C>G), RS1003021641 (16:89202767 G>A,C), RS1003162191 (16:89199106 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): 16q24.3 microdeletion syndrome (MONDO:0016838)

Orphanet (1): 16q24.3 microdeletion syndrome (Orphanet:261250)

HPO phenotypes

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

GWAS associations

0 associations (top):

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 or poorly characterized SLC22 family members

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects expression, decreases expression	2
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases expression	1
Folic Acid	decreases expression	1
Triclosan	increases expression	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Copper Sulfate	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4J1	HCT116-SLC22A31-KO-c12	Cancer cell line	Male
CVCL_D4J2	HCT116-SLC22A31-KO-c80	Cancer cell line	Male

Clinical trials (associated diseases)

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