SLC67A2

Summary

SLC67A2 (solute carrier family 67 member 2, HGNC:28158) is a protein-coding gene on chromosome 2q12.1, encoding Solute carrier family 67 member A2 (Q8NBP5).

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

Source: NCBI Gene 84804 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 90 total
• MANE Select transcript: NM_032718

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28158
Approved symbol	SLC67A2
Name	solute carrier family 67 member 2
Location	2q12.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC11332
Ensembl gene	ENSG00000135953
Ensembl biotype	protein_coding
OMIM	620301
Entrez	84804

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 nonsense_mediated_decay, 4 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000258436, ENST00000411991, ENST00000421966, ENST00000428085, ENST00000437075, ENST00000438943, ENST00000462099, ENST00000496253, ENST00000869175, ENST00000939979, ENST00000962756

RefSeq mRNA: 3 — MANE Select: NM_032718 NM_001322080, NM_001322081, NM_032718

CCDS: CCDS2063

Canonical transcript exons

ENST00000258436 — 6 exons

Exon	Start	End
ENSE00001163854	102714630	102719207
ENSE00001947537	102736646	102736888
ENSE00003480138	102731025	102731068
ENSE00003536320	102723700	102723909
ENSE00003558209	102726845	102726974
ENSE00003613105	102732322	102732409

Expression profiles

Bgee: expression breadth ubiquitous, 218 present calls, max score 85.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.0729 / max 74.3740, expressed in 1402 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
29991	3.0729	1402

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tendon of biceps brachii	UBERON:0008188	85.34	gold quality
mucosa of transverse colon	UBERON:0004991	84.11	gold quality
endometrium epithelium	UBERON:0004811	83.14	gold quality
body of pancreas	UBERON:0001150	82.26	gold quality
rectum	UBERON:0001052	82.19	gold quality
paraflocculus	UBERON:0005351	82.06	silver quality
jejunal mucosa	UBERON:0000399	81.41	gold quality
right lobe of liver	UBERON:0001114	81.22	gold quality
pancreas	UBERON:0001264	80.47	gold quality
bone marrow cell	CL:0002092	80.30	gold quality
frontal pole	UBERON:0002795	80.29	gold quality
duodenum	UBERON:0002114	80.01	gold quality
endothelial cell	CL:0000115	79.94	gold quality
granulocyte	CL:0000094	79.37	gold quality
middle frontal gyrus	UBERON:0002702	79.36	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.31	gold quality
transverse colon	UBERON:0001157	78.95	gold quality
ganglionic eminence	UBERON:0004023	78.67	gold quality
cortical plate	UBERON:0005343	78.34	gold quality
islet of Langerhans	UBERON:0000006	78.15	gold quality
body of stomach	UBERON:0001161	77.82	gold quality
liver	UBERON:0002107	77.61	gold quality
cerebellar cortex	UBERON:0002129	77.60	gold quality
cerebellar hemisphere	UBERON:0002245	77.57	gold quality
Brodmann (1909) area 10	UBERON:0013541	77.57	gold quality
cerebellum	UBERON:0002037	77.39	gold quality
stromal cell of endometrium	CL:0002255	77.15	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.02	gold quality
small intestine	UBERON:0002108	76.95	gold quality
esophagus mucosa	UBERON:0002469	76.86	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.83

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting SLC67A2, 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-340-5P	100.00	72.50	4437
HSA-MIR-3120-5P	100.00	65.56	965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-8063	99.91	69.76	3146

Literature-anchored findings (GeneRIF, showing 1)

• propose MFSD4A and MFSD9 to be novel transporters, belonging to disparate SLC families. Both proteins were located to neurons in mouse brain, and their mRNA expression levels were affected by the diet (PMID:29049335)

Cross-species orthologs

11 orthologs

Organism	Symbol	Gene ID
danio_rerio	mfsd9	ENSDARG00000074728
mus_musculus	Mfsd9	ENSMUSG00000041945
rattus_norvegicus	Mfsd9	ENSRNOG00000023129
caenorhabditis_elegans		WBGENE00010182
caenorhabditis_elegans		WBGENE00010282
caenorhabditis_elegans		WBGENE00012222
caenorhabditis_elegans		WBGENE00016093
caenorhabditis_elegans		WBGENE00016094
caenorhabditis_elegans		WBGENE00016095
caenorhabditis_elegans		WBGENE00017861
caenorhabditis_elegans		WBGENE00021814

Paralogs (6): MFSD10 (ENSG00000109736), MFSD1 (ENSG00000118855), MFSD14B (ENSG00000148110), MFSD14A (ENSG00000156875), MFSD8 (ENSG00000164073), MFSD5 (ENSG00000182544)

Protein

Protein identifiers

Solute carrier family 67 member A2 — Q8NBP5 (reviewed: Q8NBP5)

Alternative names: Major facilitator superfamily domain-containing protein 9

All UniProt accessions (5): Q8NBP5, F2Z2A2, F8WDV5, F8WE00, H7C3S7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

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

RefSeq proteins (3): NP_001309009, NP_001309010, NP_116107* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001958	Tet-R_TetA/multi-R_MdtG-like	Family
IPR005829	Sugar_transporter_CS	Conserved_site
IPR011701	MFS	Family
IPR020846	MFS_dom	Domain
IPR036259	MFS_trans_sf	Homologous_superfamily

Pfam: PF07690

UniProt features (19 total): transmembrane region 9, sequence variant 5, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NBP5-F1	80.84	0.56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 58 (showing top): chr2q12, HOEGERKORP_CD44_TARGETS_DIRECT_UP, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, GOBP_TRANSMEMBRANE_TRANSPORT, SCGGAAGY_ELK1_02, GOMF_TRANSPORTER_ACTIVITY, WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP, CHYLA_CBFA2T3_TARGETS_DN, FEVR_CTNNB1_TARGETS_UP, TERAO_AOX4_TARGETS_HG_UP, ZWANG_DOWN_BY_2ND_EGF_PULSE, STK33_SKM_UP, FOXN3_TARGET_GENES, TRIP13_TARGET_GENES, ZNF618_TARGET_GENES

GO Biological Process (1): 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	1
cellular process	1
transporter activity	1
transmembrane transport	1
cellular anatomical structure	1

Protein interactions and networks

STRING

573 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC67A2	SVOPL	Q8N434	708
SLC67A2	MFSD6	Q6ZSS7	703
SLC67A2	UNC93A	Q86WB7	692
SLC67A2	SLC61A1	Q6N075	692
SLC67A2	SVOP	Q8N4V2	676
SLC67A2	MFSD11	O43934	670
SLC67A2	TMEM182	Q6ZP80	666
SLC67A2	SLC68A1	Q14CX5	665
SLC67A2	MFSD6L	Q8IWD5	652
SLC67A2	SPNS1	Q9H2V7	643
SLC67A2	MFSD12	Q6NUT3	639
SLC67A2	SLC33A2	Q96ES6	624
SLC67A2	SPNS3	Q6ZMD2	591
SLC67A2	MFSD1	Q9H3U5	566
SLC67A2	AAGAB	Q6PD74	563

IntAct

11 interactions, top by confidence:

A	B	Type	Score
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
APLNR	METTL15	psi-mi:“MI:0914”(association)	0.530
TTYH1	TMEM223	psi-mi:“MI:0914”(association)	0.350
TSPAN15	TMEM223	psi-mi:“MI:0914”(association)	0.350
GPR12	TLCD2	psi-mi:“MI:0914”(association)	0.350
SLC2A9	HIP1R	psi-mi:“MI:0914”(association)	0.350
MFSD8	STXBP3	psi-mi:“MI:0914”(association)	0.350
MFSD9	PGRMC1	psi-mi:“MI:0914”(association)	0.350
RHBG	PEDS1	psi-mi:“MI:0914”(association)	0.350

BioGRID (64): MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Proximity Label-MS), MFSD9 (Affinity Capture-MS), MFSD9 (Affinity Capture-MS), ABHD16A (Affinity Capture-MS), ACADSB (Affinity Capture-MS), CD97 (Affinity Capture-MS), AGK (Affinity Capture-MS)

ESM2 similar proteins: A1Z7R6, A2AWR3, A4IF94, A4IHK6, A5D7V7, B2RXV4, B2RYH9, O75387, P34711, P42557, P58355, P70187, Q09428, Q0P5V9, Q0VCM6, Q4LE88, Q5BK75, Q5BKX6, Q5F4B8, Q5RBM3, Q5RF58, Q5SR56, Q7Z3Q1, Q866G7, Q8BIV7, Q8BSM7, Q8C0T7, Q8CA03, Q8CGA3, Q8CIA9, Q8HYW2, Q8K0H7, Q8K4S3, Q8N370, Q8NBP5, Q8R3L5, Q96MC6, Q99624, Q99N02, Q9BY10

Diamond homologs: A0A0U2UXG3, A0A254TZW7, A0A345BJP9, A0A348HAX9, A0A348HAY7, A0A3G1DIQ9, B8MKZ1, B8MKZ7, G3Y4N5, O34307, P38227, P40474, P40475, P53943, Q0D153, Q59YT1, Q5A6P6, Q6FNQ2, Q6FSQ7, Q8NBP5, A0A0C1C354, A0A0D1DYJ6, A0A0E3D8L1, A0A0F9XXG3, A0A0N7D7C9, A0A0U5GJZ5, A0A140JWS3, A0A142I724, A0A1L9WQV4, A0A1V6PBC8, A0A1W5T3J9, A0A2I1C3U4, A0A2L0P0L8, A0A2Z1U8L7, A0A3G1DJE2, A0A3G9H2R5, A0A411KUX1, A0A443HJZ5, A0A455ZIM6, A0A4P8DK16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	74
Likely benign	4
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1065 predictions. Top by Δscore:

Variant	Effect	Δscore
2:102731024:CCA:C	donor_gain	1.0000
2:102719185:CCA:C	acceptor_gain	0.9900
2:102719186:C:CT	acceptor_gain	0.9900
2:102719186:C:T	acceptor_gain	0.9900
2:102719187:A:C	acceptor_gain	0.9900
2:102723695:CTT:C	donor_loss	0.9900
2:102723696:TTA:T	donor_loss	0.9900
2:102723697:T:TG	donor_loss	0.9900
2:102723698:A:AC	donor_gain	0.9900
2:102723699:C:CC	donor_gain	0.9900
2:102723699:CCAG:C	donor_gain	0.9900
2:102731017:TAAC:T	donor_loss	0.9900
2:102731018:AACT:A	donor_loss	0.9900
2:102731020:CTTA:C	donor_loss	0.9900
2:102731021:T:TA	donor_loss	0.9900
2:102731022:TACCA:T	donor_loss	0.9900
2:102731023:A:AT	donor_loss	0.9900
2:102731065:GAGCC:G	acceptor_loss	0.9900
2:102731066:AGCCT:A	acceptor_loss	0.9900
2:102731067:GCC:G	donor_loss	0.9900
2:102731067:GCCT:G	acceptor_loss	0.9900
2:102731068:CCT:C	donor_loss	0.9900
2:102731068:CCTGT:C	acceptor_loss	0.9900
2:102731069:C:CC	acceptor_gain	0.9900
2:102731069:CTGTA:C	donor_loss	0.9900
2:102731070:T:G	acceptor_loss	0.9900
2:102732314:CCACT:C	donor_loss	0.9900
2:102732315:CACTC:C	donor_loss	0.9900
2:102732316:ACTCA:A	donor_loss	0.9900
2:102732317:CTCAC:C	donor_loss	0.9900

AlphaMissense

3034 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:102718867:A:C	S326R	0.995
2:102718867:A:T	S326R	0.995
2:102718869:T:G	S326R	0.995
2:102732392:G:C	S61R	0.995
2:102732392:G:T	S61R	0.995
2:102732394:T:G	S61R	0.995
2:102726915:A:C	S119R	0.994
2:102726915:A:T	S119R	0.994
2:102726917:T:G	S119R	0.994
2:102731034:G:C	S96R	0.990
2:102731034:G:T	S96R	0.990
2:102731036:T:G	S96R	0.990
2:102723899:T:A	K146N	0.989
2:102723899:T:G	K146N	0.989
2:102723900:T:A	K146I	0.989
2:102723790:C:G	G183R	0.988
2:102723797:G:C	F180L	0.988
2:102723797:G:T	F180L	0.988
2:102723799:A:G	F180L	0.988
2:102723801:C:T	G179D	0.987
2:102726963:G:C	S103R	0.986
2:102726963:G:T	S103R	0.986
2:102726965:T:G	S103R	0.986
2:102732399:C:T	G59D	0.986
2:102736654:C:G	G53R	0.985
2:102723789:C:T	G183D	0.984
2:102732400:C:G	G59R	0.984
2:102718577:C:G	R423P	0.982
2:102723725:G:C	C204W	0.981
2:102732393:C:A	S61I	0.981

dbSNP variants (sampled 300 via entrez): RS1000198734 (2:102718725 T>C), RS1000253993 (2:102724749 C>T), RS1000367431 (2:102729059 C>T), RS1000477363 (2:102735130 T>C), RS1000614195 (2:102737364 T>C), RS1000622596 (2:102724535 A>C,G), RS1000862286 (2:102728759 C>T), RS1000914466 (2:102731494 G>T), RS1001279197 (2:102734833 T>A,C), RS1001439064 (2:102728344 A>G), RS1001538461 (2:102718134 C>A,G,T), RS1001640444 (2:102717170 C>T), RS1001914916 (2:102735795 A>G), RS1002276278 (2:102717381 G>A,C), RS1002283159 (2:102736133 C>T)

Disease associations

OMIM: gene MIM:620301 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001651_87	Response to amphetamines	5.000000e-06
GCST001859_48	Thiazide-induced adverse metabolic effects in hypertensive patients	6.000000e-06
GCST003542_105	Night sleep phenotypes	9.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, increases expression	3
trichostatin A	decreases expression	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, increases expression, increases abundance	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
nickel sulfate	increases expression	1
resorcinol	decreases expression	1
methacrylaldehyde	increases abundance, affects cotreatment, increases expression	1
entinostat	decreases expression	1
abrine	decreases expression	1
(+)-JQ1 compound	increases expression	1
Acrolein	increases expression, increases abundance, affects cotreatment	1
Air Pollutants	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	increases mutagenesis	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Phenylmercuric Acetate	decreases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Tobacco Smoke Pollution	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Volatile Organic Compounds	affects cotreatment, increases expression	1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4GW	HCT116-MFSD9-KO-c12	Cancer cell line	Male
CVCL_D4GX	HCT116-MFSD9-KO-c9	Cancer cell line	Male
CVCL_SY23	HAP1 MFSD9 (-) 1	Cancer cell line	Male
CVCL_XQ50	HAP1 MFSD9 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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