SLC35F4

Summary

SLC35F4 (solute carrier family 35 member F4, HGNC:19845) is a protein-coding gene on chromosome 14q22.3-q23.1, encoding Solute carrier family 35 member F4 (A4IF30). Putative solute transporter.

Predicted to be located in membrane.

Source: NCBI Gene 341880 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_001306087

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19845
Approved symbol	SLC35F4
Name	solute carrier family 35 member F4
Location	14q22.3-q23.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37712
Ensembl gene	ENSG00000151812
Ensembl biotype	protein_coding
Entrez	341880

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000339762, ENST00000554648, ENST00000554729, ENST00000556306, ENST00000556568, ENST00000556826, ENST00000557254, ENST00000557430

RefSeq mRNA: 6 — MANE Select: NM_001306087 NM_001206920, NM_001306087, NM_001352012, NM_001352013, NM_001352014, NM_001352015

CCDS: CCDS76684, CCDS86392

Canonical transcript exons

ENST00000556826 — 8 exons

Exon	Start	End
ENSE00001094549	57581214	57581433
ENSE00002499966	57865723	57866092
ENSE00003467638	57593939	57594124
ENSE00003470364	57589216	57589513
ENSE00003513657	57566475	57566564
ENSE00003555806	57571894	57572019
ENSE00003608269	57569788	57569980
ENSE00003894478	57563920	57564376

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 84.74.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2319 / max 92.1669, expressed in 68 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143415	0.0605	24
143411	0.0501	20
143412	0.0425	13
143413	0.0224	8
143414	0.0196	4
143410	0.0179	8
143409	0.0146	6
143418	0.0042	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	84.74	gold quality
cerebellar cortex	UBERON:0002129	84.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	83.94	gold quality
cerebellum	UBERON:0002037	83.50	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.50	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.59	gold quality
islet of Langerhans	UBERON:0000006	70.26	gold quality
cerebellar vermis	UBERON:0004720	66.13	gold quality
sperm	CL:0000019	65.17	silver quality
nucleus accumbens	UBERON:0001882	64.97	gold quality
pancreatic ductal cell	CL:0002079	63.44	silver quality
prostate gland	UBERON:0002367	63.11	gold quality
hypothalamus	UBERON:0001898	62.48	gold quality
body of uterus	UBERON:0009853	62.26	gold quality
caudate nucleus	UBERON:0001873	61.65	gold quality
prefrontal cortex	UBERON:0000451	61.14	gold quality
cortical plate	UBERON:0005343	60.12	gold quality
seminal vesicle	UBERON:0000998	59.64	gold quality
putamen	UBERON:0001874	58.89	gold quality
lower lobe of lung	UBERON:0008949	58.65	silver quality
left lobe of thyroid gland	UBERON:0001120	58.17	gold quality
tibialis anterior	UBERON:0001385	58.13	silver quality
pons	UBERON:0000988	57.67	gold quality
myometrium	UBERON:0001296	57.41	gold quality
thyroid gland	UBERON:0002046	57.06	gold quality
gall bladder	UBERON:0002110	57.05	gold quality
primary visual cortex	UBERON:0002436	56.95	gold quality
mucosa of stomach	UBERON:0001199	56.64	gold quality
brain	UBERON:0000955	56.38	gold quality
right frontal lobe	UBERON:0002810	55.82	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.87
E-MTAB-6386	no	11.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting SLC35F4, 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-513A-5P	100.00	69.77	2465
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-205-3P	99.92	69.92	3165
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-5580-3P	99.70	69.41	2052
HSA-MIR-6073	99.60	70.36	793
HSA-MIR-6074	98.89	69.64	2187
HSA-MIR-502-5P	98.77	66.51	906

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc35f4	ENSDARG00000103124
mus_musculus	Slc35f4	ENSMUSG00000021852
rattus_norvegicus	Slc35f4	ENSRNOG00000014982
drosophila_melanogaster	CG42322	FBGN0259222
caenorhabditis_elegans		WBGENE00022252

Paralogs (1): SLC35F3 (ENSG00000183780)

Protein

Protein identifiers

Solute carrier family 35 member F4 — A4IF30 (reviewed: A4IF30)

All UniProt accessions (4): A4IF30, G3V2S4, G3V4Z9, H0YJV4

UniProt curated annotations — full annotation on UniProt →

Function. Putative solute transporter.

Subcellular location. Membrane.

Similarity. Belongs to the SLC35F solute transporter family.

Isoforms (2)

UniProt ID	Names	Canonical?
A4IF30-1	1	yes
A4IF30-2	2

RefSeq proteins (6): NP_001193849, NP_001293016, NP_001338941, NP_001338942, NP_001338943, NP_001338944 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000620	EamA_dom	Domain
IPR026505	Solute_c_fam_35_mem_F3/F4	Family
IPR037185	EmrE-like	Homologous_superfamily

Pfam: PF00892

UniProt features (13 total): transmembrane region 10, chain 1, domain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A4IF30-F1	67.19	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): chr14q23, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, SRC_UP.V1_UP, CAHOY_NEURONAL, SOX3_TARGET_GENES, MIR27A_3P_MIR27B_3P, MIR9985, MIR205_3P, MIR513A_5P, MIR6074, MIR6790_5P, MIR4658, MIR6767_3P, DESCARTES_MAIN_FETAL_INHIBITORY_INTERNEURONS

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

362 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC35F4	OR2B3	O76000	665
SLC35F4	CCDC198	Q9NVL8	644
SLC35F4	TMEM268	Q5VZI3	614
SLC35F4	TMEM196	Q5HYL7	596
SLC35F4	TMEM266	Q2M3C6	591
SLC35F4	OR10G6	Q8NH81	575
SLC35F4	TSR3	Q9UJK0	544
SLC35F4	KLHL25	Q9H0H3	529
SLC35F4	DHX40	Q8IX18	508
SLC35F4	STARD3NL	O95772	480
SLC35F4	ANAPC13	Q9BS18	474
SLC35F4	CDC42SE2	Q9NRR3	471
SLC35F4	BUD13	Q9BRD0	432
SLC35F4	OR8B8	Q15620	419
SLC35F4	GPR19	Q15760	389

IntAct

3 interactions, top by confidence:

A	B	Type	Score
DND1	RPSA2	psi-mi:“MI:0914”(association)	0.350
SLC35F4	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (221): ABCF1 (Affinity Capture-MS), ABI1 (Affinity Capture-MS), AGRN (Affinity Capture-MS), AHNAK (Affinity Capture-MS), AKAP9 (Affinity Capture-MS), ALYREF (Affinity Capture-MS), AP3B1 (Affinity Capture-MS), APC (Affinity Capture-MS), APEX1 (Affinity Capture-MS), ARID1A (Affinity Capture-MS), ASCC3 (Affinity Capture-MS), ASH2L (Affinity Capture-MS), ATF7IP (Affinity Capture-MS), ATXN2 (Affinity Capture-MS), BOD1L1 (Affinity Capture-MS)

ESM2 similar proteins: A1L272, A2RV80, A4IF30, A6QL92, A6QPI1, O02777, O80605, P17200, P20272, P21554, P47746, P51810, P56971, P70259, Q1LZI2, Q2V4F9, Q3TDN0, Q3UGM2, Q4R794, Q5F383, Q5FVJ3, Q5IS73, Q5R4D7, Q5R6J3, Q5RD30, Q66H88, Q6P0E8, Q6P499, Q6R5J2, Q71SP5, Q8BGN5, Q8BZK4, Q8CBH5, Q8IY50, Q8NA31, Q8NBV4, Q8R314, Q8RWF4, Q8WV83, Q91WB2

Diamond homologs: A4IF30, Q1LZI2, Q8BZK4, Q8IY50

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2548 predictions. Top by Δscore:

Variant	Effect	Δscore
14:57564372:CACAG:C	acceptor_gain	1.0000
14:57564373:ACAG:A	acceptor_gain	1.0000
14:57564374:CAG:C	acceptor_gain	1.0000
14:57564374:CAGC:C	acceptor_gain	1.0000
14:57564375:AG:A	acceptor_gain	1.0000
14:57564377:C:CC	acceptor_gain	1.0000
14:57564378:T:A	acceptor_loss	1.0000
14:57571889:CATA:C	donor_loss	1.0000
14:57571890:ATAC:A	donor_loss	1.0000
14:57571891:TACCT:T	donor_loss	1.0000
14:57571892:A:T	donor_loss	1.0000
14:57571893:C:T	donor_loss	1.0000
14:57584409:C:A	donor_gain	1.0000
14:57589358:CAAT:C	donor_gain	1.0000
14:57865721:A:AC	donor_gain	1.0000
14:57865722:C:CC	donor_gain	1.0000
14:57865722:CTTTT:C	donor_gain	1.0000
14:57564373:ACAGC:A	acceptor_gain	0.9900
14:57564374:CAGCT:C	acceptor_gain	0.9900
14:57564375:AGCT:A	acceptor_gain	0.9900
14:57564376:GCT:G	acceptor_gain	0.9900
14:57564377:CTAGG:C	acceptor_gain	0.9900
14:57566561:AAGGC:A	acceptor_loss	0.9900
14:57566563:GGC:G	acceptor_loss	0.9900
14:57566564:GC:G	acceptor_loss	0.9900
14:57566565:C:CA	acceptor_loss	0.9900
14:57566565:C:CC	acceptor_gain	0.9900
14:57566566:T:G	acceptor_loss	0.9900
14:57572016:CTAT:C	acceptor_gain	0.9900
14:57580440:T:TA	donor_gain	0.9900

AlphaMissense

3158 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:57571992:C:G	G315R	1.000
14:57581371:G:T	A253D	1.000
14:57564275:A:G	W476R	0.999
14:57564275:A:T	W476R	0.999
14:57564300:A:C	F467L	0.999
14:57564300:A:T	F467L	0.999
14:57564302:A:G	F467L	0.999
14:57564304:C:T	G466E	0.999
14:57564305:C:A	G466W	0.999
14:57564305:C:G	G466R	0.999
14:57564305:C:T	G466R	0.999
14:57566489:A:T	V437D	0.999
14:57566491:G:C	S436R	0.999
14:57566491:G:T	S436R	0.999
14:57566493:T:G	S436R	0.999
14:57569913:C:T	G370D	0.999
14:57569914:C:G	G370R	0.999
14:57571904:G:T	A344E	0.999
14:57571916:G:T	A340D	0.999
14:57571991:C:T	G315D	0.999
14:57572012:G:T	A308D	0.999
14:57581227:A:G	F301S	0.999
14:57581239:A:G	L297P	0.999
14:57581249:A:G	W294R	0.999
14:57581249:A:T	W294R	0.999
14:57581254:A:G	L292P	0.999
14:57581279:A:G	C284R	0.999
14:57589298:A:G	W205R	0.999
14:57589298:A:T	W205R	0.999
14:57589313:A:G	W200R	0.999

dbSNP variants (sampled 300 via entrez): RS1000003450 (14:57786900 C>T), RS1000009218 (14:57672954 A>C), RS1000017643 (14:57655835 T>C,G), RS1000022986 (14:57825032 C>G), RS1000029500 (14:57633843 G>T), RS1000034258 (14:57799619 A>G), RS1000034641 (14:57596097 G>T), RS1000037124 (14:57864085 A>T), RS1000040609 (14:57965197 C>T), RS1000051802 (14:57711985 G>A,T), RS1000056890 (14:57729838 A>G), RS1000058550 (14:57696555 C>G,T), RS1000060331 (14:57934271 G>A,T), RS1000060657 (14:57713170 T>C), RS1000061883 (14:57576756 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST003126_7	Influenza A (H1N1) severity	2.000000e-06
GCST003542_118	Night sleep phenotypes	1.000000e-06
GCST003875_12	Gut microbiota (bacterial taxa)	9.000000e-10
GCST004101_3	Body mass index (change over time) in gastrointestinal cancer	9.000000e-06
GCST004797_9	Brain volume in infants (grey matter)	8.000000e-07

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007743	influenza A severity measurement
EFO:0007874	gut microbiome measurement
EFO:0007883	taxonomic microbiome measurement
EFO:0005937	longitudinal BMI measurement
EFO:0008368	infant grey matter volume measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs74832512	SLC35F4		0.00	0

GtoPdb / IUPHAR curated pharmacology

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

Target class: transporter — SLC35 family of nucleotide sugar transporters

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	decreases expression, affects cotreatment	2
thallium sulfate	increases expression	1
sodium arsenite	affects methylation	1
aflatoxin B2	increases methylation	1
Benzo(a)pyrene	affects methylation	1
Copper	decreases expression, affects cotreatment	1
Phthalic Acids	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Valproic Acid	decreases methylation	1
Aflatoxin B1	decreases methylation	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D4EA	HEK-SLC35F4-KO-c7	Transformed cell line	Female

Clinical trials (associated diseases)

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