SLC49A3

Summary

SLC49A3 (solute carrier family 49 member 3, HGNC:26177) is a protein-coding gene on chromosome 4p16.3, encoding Solute carrier family 49 member A3 (Q6UXD7).

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

Source: NCBI Gene 84179 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 141 total
• MANE Select transcript: NM_032219

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26177
Approved symbol	SLC49A3
Name	solute carrier family 49 member 3
Location	4p16.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22269, LP2561
Ensembl gene	ENSG00000169026
Ensembl biotype	protein_coding
OMIM	620318
Entrez	84179

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 15 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000322224, ENST00000347950, ENST00000404286, ENST00000503156, ENST00000507165, ENST00000512249, ENST00000512400, ENST00000513740, ENST00000515118, ENST00000894934, ENST00000894935, ENST00000894936, ENST00000894937, ENST00000894938, ENST00000931981, ENST00000965819, ENST00000965820

RefSeq mRNA: 7 — MANE Select: NM_032219 NM_001294341, NM_001294342, NM_001378059, NM_001378060, NM_001378061, NM_001378062, NM_032219

CCDS: CCDS3338, CCDS75086, CCDS77883, CCDS93459

Canonical transcript exons

ENST00000322224 — 10 exons

Exon	Start	End
ENSE00001166720	684483	684599
ENSE00001166726	684719	684856
ENSE00001224245	685835	685911
ENSE00001224256	686089	686302
ENSE00001870500	688993	689151
ENSE00003468729	686532	686690
ENSE00003629762	682781	682890
ENSE00003635635	683609	683761
ENSE00003652240	683210	683367
ENSE00003678613	681829	682376

Expression profiles

Bgee: expression breadth ubiquitous, 168 present calls, max score 89.45.

FANTOM5 (CAGE): breadth broad, TPM avg 3.0316 / max 117.4482, expressed in 830 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
51000	1.4911	309
51001	1.3865	704
50998	0.0559	11
50996	0.0483	13
50999	0.0423	7
50997	0.0076	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	89.45	gold quality
left testis	UBERON:0004533	87.95	gold quality
right testis	UBERON:0004534	87.19	gold quality
monocyte	CL:0000576	86.81	gold quality
mononuclear cell	CL:0000842	86.48	gold quality
right lobe of thyroid gland	UBERON:0001119	86.33	gold quality
leukocyte	CL:0000738	85.96	gold quality
granulocyte	CL:0000094	85.89	gold quality
metanephros cortex	UBERON:0010533	85.43	gold quality
minor salivary gland	UBERON:0001830	85.39	gold quality
left lobe of thyroid gland	UBERON:0001120	85.20	gold quality
body of stomach	UBERON:0001161	84.81	gold quality
right atrium auricular region	UBERON:0006631	84.71	gold quality
skin of abdomen	UBERON:0001416	84.08	gold quality
testis	UBERON:0000473	83.39	gold quality
upper lobe of left lung	UBERON:0008952	83.38	gold quality
omental fat pad	UBERON:0010414	83.12	gold quality
peritoneum	UBERON:0002358	83.00	gold quality
thyroid gland	UBERON:0002046	82.86	gold quality
spleen	UBERON:0002106	82.55	gold quality
buccal mucosa cell	CL:0002336	82.45	gold quality
right lung	UBERON:0002167	82.31	gold quality
skin of leg	UBERON:0001511	81.94	gold quality
mucosa of transverse colon	UBERON:0004991	81.94	gold quality
lower esophagus mucosa	UBERON:0035834	81.89	gold quality
cardiac atrium	UBERON:0002081	81.70	gold quality
ascending aorta	UBERON:0001496	81.60	gold quality
thoracic aorta	UBERON:0001515	81.58	gold quality
descending thoracic aorta	UBERON:0002345	81.51	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting SLC49A3, 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-3665	97.73	65.08	975
HSA-MIR-4800-5P	97.22	65.91	324
HSA-MIR-1281	92.96	65.73	260

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
mus_musculus	Slc49a3	ENSMUSG00000029490
rattus_norvegicus	Slc49a3	ENSRNOG00000023937
caenorhabditis_elegans		WBGENE00007347
caenorhabditis_elegans		WBGENE00015181
caenorhabditis_elegans		WBGENE00016586

Paralogs (4): FLVCR2 (ENSG00000119686), SLC49A4 (ENSG00000138463), FLVCR1 (ENSG00000162769), CFAP276 (ENSG00000179902)

Protein

Protein identifiers

Solute carrier family 49 member A3 — Q6UXD7 (reviewed: Q6UXD7)

Alternative names: Major facilitator superfamily domain-containing protein 7, Myosin light polypeptide 5 regulatory protein

All UniProt accessions (5): Q6UXD7, D6R9R0, D6RB07, D6RED0, D6RIZ6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the major facilitator superfamily.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6UXD7-1	1	yes
Q6UXD7-2	2
Q6UXD7-3	3

RefSeq proteins (7): NP_001281270, NP_001281271, NP_001364988, NP_001364989, NP_001364990, NP_001364991, NP_115595* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011701	MFS	Family
IPR036259	MFS_trans_sf	Homologous_superfamily
IPR049680	FLVCR1-2_SLC49-like	Family

Pfam: PF07690

UniProt features (21 total): transmembrane region 12, splice variant 3, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UXD7-F1	75.37	0.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 36 (showing top): chr4p16, GOBP_TRANSMEMBRANE_TRANSPORT, GOMF_TRANSPORTER_ACTIVITY, HATADA_METHYLATED_IN_LUNG_CANCER_UP, LIM_MAMMARY_STEM_CELL_DN, RAPA_EARLY_UP.V1_DN, JNK_DN.V1_DN, IL21_UP.V1_UP, NFE2L1_TARGET_GENES, ZIM3_TARGET_GENES, ZNF184_TARGET_GENES, ZNF7_TARGET_GENES, GSE11864_CSF1_IFNG_VS_CSF1_PAM3CYS_IN_MAC_UP, MIR1281, MEBARKI_HCC_PROGENITOR_FZD8CRD_DN

GO Biological Process (1): transmembrane transport (GO:0055085)

GO Molecular Function (2): transmembrane transporter activity (GO:0022857), 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	1
cellular process	1
transporter activity	1
transmembrane transport	1
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

708 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC49A3	TBRG4	Q969Z0	589
SLC49A3	PIGG	Q5H8A4	551
SLC49A3	MFSD1	Q9H3U5	512
SLC49A3	CPLX1	O14810	487
SLC49A3	GAK	O14976	464
SLC49A3	SLC3A2	P08195	451
SLC49A3	MFSD8	Q8NHS3	448
SLC49A3	PCGF3	Q3KNV8	443
SLC49A3	SLC29A3	Q9BZD2	419
SLC49A3	ENKD1	Q9H0I2	417
SLC49A3	CCDC198	Q9NVL8	375
SLC49A3	DEFB130A	P0DP74	352
SLC49A3	PM20D2	Q8IYS1	345
SLC49A3	ATP5ME	P56385	336
SLC49A3	PDE6B	P35913	324

IntAct

3 interactions, top by confidence:

A	B	Type	Score
SLC49A3	SLC4A1	psi-mi:“MI:0914”(association)	0.350
SLC52A1	CLGN	psi-mi:“MI:0914”(association)	0.350

BioGRID (19): MFSD7 (Two-hybrid), MFSD7 (Two-hybrid), MFSD7 (Affinity Capture-RNA), ABCC10 (Affinity Capture-MS), BAG6 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), FAM189B (Affinity Capture-MS), FZD8 (Affinity Capture-MS), GGT7 (Affinity Capture-MS), HM13 (Affinity Capture-MS), IGF2R (Affinity Capture-MS), LRFN1 (Affinity Capture-MS), PDE3B (Affinity Capture-MS), SARAF (Affinity Capture-MS), SLC4A1 (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q2HW92, A6NDV4, A6NFX1, A6QLK4, B1AWJ5, F1NCD6, F1NJ67, F1PZV2, O35308, O35595, O70461, O95907, Q08DX7, Q0IHM1, Q0P5C0, Q0P5M9, Q13286, Q14728, Q29611, Q2YDU8, Q3T9M1, Q3U481, Q501I9, Q5R8G5, Q5R9A1, Q5U419, Q60HH0, Q61124, Q66H95, Q6NUT3, Q6UXD7, Q6ZMD2, Q7RTT9, Q8BFQ6, Q8CE47, Q8NA29, Q8R0G7, Q8R139, Q8TB61, Q8VCW4

Diamond homologs: Q11073, Q28FF3, Q503P5, Q6UXD7, Q8CE47, B2RXV4, Q9ES43, Q9N1F2, Q9Y5Y0, Q4H425, A0A0R4ILB2, A0A8M9Q308, O01735, P60815, Q501I9, Q66H95, Q6GNV7, Q8BFQ6, Q91X85, Q96SL1, Q9UPI3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	117
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2260 predictions. Top by Δscore:

Variant	Effect	Δscore
4:683208:ACC:A	donor_gain	1.0000
4:683209:CCC:C	donor_gain	1.0000
4:683626:AGG:A	donor_gain	1.0000
4:684482:CA:C	donor_gain	1.0000
4:684718:CCAG:C	donor_gain	1.0000
4:686088:CA:C	donor_gain	1.0000
4:686526:ACTC:A	donor_loss	1.0000
4:686528:TCA:T	donor_loss	1.0000
4:686529:CAC:C	donor_loss	1.0000
4:686530:A:AC	donor_gain	1.0000
4:686530:ACCG:A	donor_gain	1.0000
4:686531:C:CT	donor_gain	1.0000
4:686531:C:T	donor_loss	1.0000
4:686531:CCG:C	donor_gain	1.0000
4:686531:CCGC:C	donor_gain	1.0000
4:686686:CACAG:C	acceptor_gain	1.0000
4:686687:ACAG:A	acceptor_gain	1.0000
4:686688:CAG:C	acceptor_gain	1.0000
4:686688:CAGC:C	acceptor_gain	1.0000
4:686691:CT:C	acceptor_loss	1.0000
4:681971:C:T	acceptor_gain	0.9900
4:683208:A:AC	donor_gain	0.9900
4:683208:AC:A	donor_gain	0.9900
4:683209:C:CC	donor_gain	0.9900
4:683209:CC:C	donor_gain	0.9900
4:683227:G:A	donor_gain	0.9900
4:683265:CG:C	donor_gain	0.9900
4:683365:CAC:C	acceptor_gain	0.9900
4:683369:T:A	acceptor_loss	0.9900
4:683384:G:T	acceptor_gain	0.9900

AlphaMissense

3555 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:686132:G:C	F155L	0.992
4:686132:G:T	F155L	0.992
4:686134:A:G	F155L	0.992
4:681966:T:A	I165N	0.987
4:681966:T:G	I165S	0.985
4:686133:A:C	F155C	0.983
4:686133:A:G	F155S	0.982
4:686679:G:C	S49R	0.975
4:686679:G:T	S49R	0.975
4:686681:T:G	S49R	0.975
4:681974:G:T	G168W	0.974
4:681966:T:C	I165T	0.972
4:686267:A:C	S110R	0.970
4:686267:A:T	S110R	0.970
4:686269:T:G	S110R	0.970
4:683254:G:C	F370L	0.969
4:683254:G:T	F370L	0.969
4:683256:A:G	F370L	0.969
4:681972:A:C	H167P	0.968
4:686137:A:G	W154R	0.966
4:686137:A:T	W154R	0.966
4:686195:G:C	S134R	0.966
4:686195:G:T	S134R	0.966
4:686197:T:G	S134R	0.966
4:684823:A:G	C207R	0.964
4:681975:G:T	G168V	0.962
4:686134:A:C	F155V	0.960
4:686134:A:T	F155I	0.954
4:681975:G:A	G168E	0.952
4:686279:G:C	N106K	0.951

dbSNP variants (sampled 300 via entrez): RS1000068123 (4:685084 C>G), RS1000226214 (4:676383 C>A,T), RS1000688157 (4:692751 A>T), RS1000845655 (4:687525 C>T), RS1000864318 (4:690058 A>G), RS1000940746 (4:683461 C>A,G,T), RS1000993214 (4:683677 T>C,G), RS1001105378 (4:679599 G>A), RS1001162977 (4:693216 C>T), RS1001208988 (4:677864 C>G,T), RS1001239522 (4:684978 C>T), RS1001299161 (4:687668 G>C,T), RS1001333124 (4:680872 T>C), RS1001385348 (4:681041 G>A,C,T), RS1001479383 (4:686035 C>G)

Disease associations

OMIM: gene MIM:620318 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

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 — SLC49 family of FLVCR-related heme transporters

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
bisphenol F	affects cotreatment, increases methylation	1
triphenyl phosphate	affects expression	1
sodium arsenite	increases expression	1
bisphenol S	affects cotreatment, increases methylation	1
jinfukang	increases expression, affects cotreatment	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	increases methylation	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Particulate Matter	increases abundance, 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_D4PL	HCT116-SLC49A3-KO-c10	Cancer cell line	Male
CVCL_D4PM	HCT116-SLC49A3-KO-c7	Cancer cell line	Male
CVCL_SY20	HAP1 MFSD7 (-) 1	Cancer cell line	Male
CVCL_SY21	HAP1 MFSD7 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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