SLC68A1

Summary

SLC68A1 (solute carrier family 68 member 1, HGNC:26196) is a protein-coding gene on chromosome 10q24.32, encoding Solute carrier family 68 member 1 (Q14CX5). May act as a cation symporter.

Located in plasma membrane.

Source: NCBI Gene 79847 — RefSeq curated summary.

At a glance

• GWAS associations: 15
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_024789

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26196
Approved symbol	SLC68A1
Name	solute carrier family 68 member 1
Location	10q24.32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22529, bA18I14.8
Ensembl gene	ENSG00000138111
Ensembl biotype	protein_coding
OMIM	620255
Entrez	79847

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 24 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000238936, ENST00000369931, ENST00000428200, ENST00000450947, ENST00000469294, ENST00000873281, ENST00000873282, ENST00000873283, ENST00000873284, ENST00000873285, ENST00000873286, ENST00000873287, ENST00000873288, ENST00000873289, ENST00000873290, ENST00000873291, ENST00000933878, ENST00000933879, ENST00000933880, ENST00000933881, ENST00000933882, ENST00000933883, ENST00000933884, ENST00000968098, ENST00000968099, ENST00000968100

RefSeq mRNA: 1 — MANE Select: NM_024789 NM_024789

CCDS: CCDS7535

Canonical transcript exons

ENST00000238936 — 10 exons

Exon	Start	End
ENSE00000722799	102473819	102474012
ENSE00000811536	102472854	102472950
ENSE00001101181	102475722	102477045
ENSE00001136054	102473570	102473741
ENSE00001136093	102470665	102471117
ENSE00001661308	102461395	102461450
ENSE00003507765	102465982	102466087
ENSE00003530771	102469993	102470075
ENSE00003560823	102471273	102471396
ENSE00003797016	102468955	102469197

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 88.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.1754 / max 68.0084, expressed in 1655 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
106722	7.1754	1655

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	88.38	gold quality
cerebellar hemisphere	UBERON:0002245	87.96	gold quality
cerebellar cortex	UBERON:0002129	87.84	gold quality
cerebellum	UBERON:0002037	86.03	gold quality
right frontal lobe	UBERON:0002810	85.12	gold quality
nucleus accumbens	UBERON:0001882	83.39	gold quality
caudate nucleus	UBERON:0001873	83.04	gold quality
granulocyte	CL:0000094	82.74	gold quality
anterior cingulate cortex	UBERON:0009835	82.74	gold quality
cingulate cortex	UBERON:0003027	82.61	gold quality
upper lobe of left lung	UBERON:0008952	82.49	gold quality
right lung	UBERON:0002167	82.37	gold quality
putamen	UBERON:0001874	82.28	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.15	gold quality
upper lobe of lung	UBERON:0008948	81.71	gold quality
skin of abdomen	UBERON:0001416	81.53	gold quality
skin of leg	UBERON:0001511	81.31	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.08	gold quality
mucosa of transverse colon	UBERON:0004991	81.07	gold quality
monocyte	CL:0000576	80.69	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.55	gold quality
mononuclear cell	CL:0000842	80.41	gold quality
right lobe of thyroid gland	UBERON:0001119	80.34	gold quality
leukocyte	CL:0000738	80.33	gold quality
cortical plate	UBERON:0005343	79.84	gold quality
prefrontal cortex	UBERON:0000451	79.79	gold quality
neocortex	UBERON:0001950	79.69	gold quality
frontal cortex	UBERON:0001870	79.31	gold quality
amygdala	UBERON:0001876	79.24	gold quality
telencephalon	UBERON:0001893	78.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	11.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

60 targeting SLC68A1, 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-5692A	100.00	74.40	6850
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-369-3P	99.85	70.52	2264
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-374C-5P	99.80	72.06	2910
HSA-MIR-655-3P	99.80	72.19	2909
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-12124	99.68	69.17	2700
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-6081	99.48	66.07	1446

Literature-anchored findings (GeneRIF, showing 3)

• The allele G of rs2001389 weakened the binding activity with CTCF, and it was related to the lower expression of a putative antioncogene MFSD13A whose knockdown promoted proliferation of PC cells. By integrating analysis on multiomics data, association studies and functional assays, we proposed that the common variant rs2001389 and the gene MFSD13A might be genetic modifiers of PC tumorigenesis. (PMID:31237042)
• Using a homology model of TMEM180, we experimentally determined that the protein has 12 transmembrane domains, and that its N-terminal and C-termini are exposed extracellularly. Moreover, we found that the putative cation-binding site of TMEM180 is conserved among orthologs, and that its position is similar to that of melibiose transporter MelB. (PMID:31615651)
• Integrative Analyses Followed by Functional Characterization Reveal TMEM180 as a Schizophrenia Risk Gene. (PMID:33768244)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	mfsd13a	ENSDARG00000009214
mus_musculus	Mfsd13a	ENSMUSG00000025227
rattus_norvegicus	Mfsd13a	ENSRNOG00000019674

Protein

Protein identifiers

Solute carrier family 68 member 1 — Q14CX5 (reviewed: Q14CX5)

Alternative names: Major facilitator superfamily domain-containing 13A, Transmembrane protein 180

All UniProt accessions (3): A0A1B0GUX1, Q14CX5, Q6UWF4

UniProt curated annotations — full annotation on UniProt →

Function. May act as a cation symporter.

Subcellular location. Cell membrane.

Tissue specificity. Highly expressed in colorectal cancer cell lines but not in the normal colonocytes.

Induction. Up-regulated under low-oxygen conditions.

RefSeq proteins (1): NP_079065* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR036259	MFS_trans_sf	Homologous_superfamily
IPR040035	TMEM180	Family

Pfam: PF13347

UniProt features (29 total): topological domain 13, transmembrane region 12, sequence conflict 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14CX5-F1	82.45	0.49

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GSE45365_NK_CELL_VS_CD11B_DC_UP, MYOGENIN_Q6, GCANCTGNY_MYOD_Q6, SANSOM_APC_TARGETS_REQUIRE_MYC, MULLIGHAN_MLL_SIGNATURE_1_UP, GEORGES_TARGETS_OF_MIR192_AND_MIR215, TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C, WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP, CHYLA_CBFA2T3_TARGETS_UP, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN, IL15_UP.V1_DN, CIITA_TARGET_GENES, SNAI1_TARGET_GENES, TOP2B_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

400 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC68A1	SLC67A2	Q8NBP5	665
SLC68A1	MFSD11	O43934	642
SLC68A1	MFSD6L	Q8IWD5	621
SLC68A1	MFSD12	Q6NUT3	606
SLC68A1	MFSD6	Q6ZSS7	603
SLC68A1	SLC61A1	Q6N075	588
SLC68A1	UNC93A	Q86WB7	578
SLC68A1	SLC75A1	Q14728	549
SLC68A1	SVOPL	Q8N434	534
SLC68A1	SVOP	Q8N4V2	528
SLC68A1	SLC33A2	Q96ES6	519
SLC68A1	SLC37A3	Q8NCC5	498
SLC68A1	FBXL15	Q9H469	490
SLC68A1	MFSD2B	A6NFX1	490
SLC68A1	SPNS3	Q6ZMD2	486

IntAct

12 interactions, top by confidence:

A	B	Type	Score
NOTCH2NLC	MFSD13A	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	MFSD13A	psi-mi:“MI:0915”(physical association)	0.560
MFSD13A	KRTAP8-1	psi-mi:“MI:0915”(physical association)	0.560
P		psi-mi:“MI:0914”(association)	0.350
MFSD13A	EXTL3	psi-mi:“MI:0914”(association)	0.350
MFSD13A	NOTCH2NLC	psi-mi:“MI:0915”(physical association)	0.000
MFSD13A	CYSRT1	psi-mi:“MI:0915”(physical association)	0.000
MFSD13A	KRTAP8-1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (14): COL1A1 (Affinity Capture-MS), GNA11 (Affinity Capture-MS), TMEM180 (Affinity Capture-MS), KRTAP8-1 (Two-hybrid), CYSRT1 (Two-hybrid), NOTCH2NL (Two-hybrid), NBPF19 (Two-hybrid), TMEM180 (Two-hybrid), EXT1 (Affinity Capture-MS), EXTL3 (Affinity Capture-MS), HMGCR (Affinity Capture-MS), YIF1B (Affinity Capture-MS), TMEM180 (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A4FV98, A5D7B1, A5PK51, A6QLN9, A8MUP2, D3ZVU9, O15527, O35595, O75078, O95848, P57775, Q05B60, Q06643, Q14728, Q14CX5, Q1LZB9, Q27HK4, Q2T9T5, Q2TBS1, Q3UGX3, Q4R3I0, Q4V892, Q58CT4, Q5E9H2, Q5RCI5, Q5SUV1, Q5TM22, Q642A6, Q6IA17, Q6PCB0, Q6XQN6, Q862Z7, Q8N8L6, Q8R2R5, Q8R2Z5, Q8R366, Q8WUG5, Q95JH0, Q95JH2, Q969P0

Diamond homologs: Q14CX5, Q58CT4, Q5ZKJ5, Q6PDE8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1643 predictions. Top by Δscore:

Variant	Effect	Δscore
10:102469159:GT:G	donor_gain	1.0000
10:102469992:GACA:G	acceptor_gain	1.0000
10:102470094:GCTC:G	donor_gain	1.0000
10:102470135:G:GT	donor_gain	1.0000
10:102470972:G:GT	donor_gain	1.0000
10:102471271:A:AG	acceptor_gain	1.0000
10:102471272:G:GG	acceptor_gain	1.0000
10:102472946:GTTGG:G	donor_gain	1.0000
10:102472947:TTGGG:T	donor_loss	1.0000
10:102472948:TGGGT:T	donor_loss	1.0000
10:102472949:GG:G	donor_gain	1.0000
10:102472949:GGGT:G	donor_loss	1.0000
10:102472950:GG:G	donor_gain	1.0000
10:102472950:GGT:G	donor_loss	1.0000
10:102472952:TGAG:T	donor_loss	1.0000
10:102472953:GAGT:G	donor_loss	1.0000
10:102473565:CCCA:C	acceptor_loss	1.0000
10:102473566:CCAGG:C	acceptor_loss	1.0000
10:102473567:CAGG:C	acceptor_loss	1.0000
10:102473568:A:AG	acceptor_gain	1.0000
10:102473568:A:C	acceptor_loss	1.0000
10:102473568:AG:A	acceptor_gain	1.0000
10:102473569:G:GG	acceptor_gain	1.0000
10:102473569:GG:G	acceptor_gain	1.0000
10:102473569:GGC:G	acceptor_gain	1.0000
10:102473569:GGCCT:G	acceptor_gain	1.0000
10:102473739:CAGG:C	donor_loss	1.0000
10:102473740:AGGTA:A	donor_loss	1.0000
10:102473741:GGTA:G	donor_loss	1.0000
10:102473742:G:C	donor_loss	1.0000

AlphaMissense

3312 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:102473974:C:A	A418D	0.999
10:102469150:T:C	F41L	0.998
10:102469152:T:A	F41L	0.998
10:102469152:T:G	F41L	0.998
10:102469183:T:C	F52L	0.998
10:102469185:C:A	F52L	0.998
10:102469185:C:G	F52L	0.998
10:102469999:T:C	F59L	0.998
10:102470001:T:A	F59L	0.998
10:102470001:T:G	F59L	0.998
10:102470008:T:A	W62R	0.998
10:102470008:T:C	W62R	0.998
10:102470014:A:C	S64R	0.998
10:102470016:C:A	S64R	0.998
10:102470016:C:G	S64R	0.998
10:102473962:G:A	G414D	0.998
10:102470013:C:A	N63K	0.997
10:102470013:C:G	N63K	0.997
10:102472881:T:C	F286L	0.997
10:102472883:C:A	F286L	0.997
10:102472883:C:G	F286L	0.997
10:102473680:A:C	S346R	0.997
10:102473682:C:A	S346R	0.997
10:102473682:C:G	S346R	0.997
10:102473838:G:C	G373R	0.997
10:102473985:G:C	G422R	0.997
10:102475886:T:A	W486R	0.997
10:102475886:T:C	W486R	0.997
10:102469184:T:C	F52S	0.996
10:102470762:T:A	W117R	0.996

dbSNP variants (sampled 300 via entrez): RS1000135735 (10:102469901 A>T), RS1000167205 (10:102470128 C>G), RS1000248149 (10:102462561 A>G), RS1000764382 (10:102463071 T>A), RS1001003571 (10:102460048 G>A), RS1001050041 (10:102474676 G>A), RS1001173642 (10:102468738 C>T), RS1001240477 (10:102473256 G>C), RS1001654739 (10:102460974 G>A), RS1002042805 (10:102473303 G>A,C), RS1002210295 (10:102459588 C>T), RS1002217887 (10:102460450 T>C), RS1002270066 (10:102460663 T>A), RS1002573837 (10:102467899 C>G), RS1002893774 (10:102463677 T>G)

Disease associations

OMIM: gene MIM:620255 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

Study	Trait	p-value
GCST001942_1	Prostate cancer	5.000000e-10
GCST003045_28	Ulcerative colitis	3.000000e-07
GCST004521_172	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_53	Autism spectrum disorder or schizophrenia	9.000000e-10
GCST005956_50	Waist-to-hip ratio adjusted for BMI	8.000000e-06
GCST005958_15	Waist-to-hip ratio adjusted for BMI (age >50)	4.000000e-06
GCST005962_36	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	6.000000e-07
GCST006409_9	Allergic rhinitis	5.000000e-18
GCST007323_15	Risk-taking tendency (4-domain principal component model)	7.000000e-09
GCST010002_298	Refractive error	3.000000e-22
GCST010703_271	Brain morphology (MOSTest)	5.000000e-13
GCST90002398_184	Neutrophil count	3.000000e-12
GCST90002400_620	Plateletcrit	2.000000e-15
GCST90002407_313	White blood cell count	7.000000e-13
GCST90020029_137	Waist circumference adjusted for body mass index	1.000000e-10

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008579	risk-taking behaviour
EFO:0004346	neuroimaging measurement
EFO:0004833	neutrophil count
EFO:0007985	platelet crit
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, affects cotreatment, increases abundance, increases expression	4
Arsenic	decreases expression, increases abundance, affects methylation, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases methylation	2
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
manganese chloride	increases abundance, affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
abrine	decreases expression	1
NSC 689534	affects binding, decreases expression	1
Acetaminophen	increases expression	1
Copper	affects binding, decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Formaldehyde	decreases expression	1
Hydrogen Peroxide	affects expression	1
Indomethacin	increases expression, affects cotreatment	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Silicon Dioxide	decreases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Thiram	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1
Acrylamide	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_D4GD	HCT116-MFSD13A-KO-c29	Cancer cell line	Male

Clinical trials (associated diseases)

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