SFT2D3

Summary

SFT2D3 (SFT2 domain containing 3, HGNC:28767) is a protein-coding gene on chromosome 2q14.3, encoding Vesicle transport protein SFT2C (Q587I9). May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex.

Predicted to be involved in protein transport and vesicle-mediated transport. Predicted to be located in several cellular components, including cytoplasm; endomembrane system; and intracellular membrane-bounded organelle.

Source: NCBI Gene 84826 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_032740

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28767
Approved symbol	SFT2D3
Name	SFT2 domain containing 3
Location	2q14.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC5391
Ensembl gene	ENSG00000173349
Ensembl biotype	protein_coding
Entrez	84826

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000310981

RefSeq mRNA: 1 — MANE Select: NM_032740 NM_032740

CCDS: CCDS2149

Canonical transcript exons

ENST00000310981 — 1 exons

Exon	Start	End
ENSE00001206349	127701497	127705242

Expression profiles

Bgee: expression breadth ubiquitous, 151 present calls, max score 89.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.1247 / max 100.1468, expressed in 1784 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
22454	12.1247	1784

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	89.27	gold quality
tibialis anterior	UBERON:0001385	84.96	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.40	gold quality
tibia	UBERON:0000979	84.26	gold quality
left ventricle myocardium	UBERON:0006566	84.15	gold quality
parotid gland	UBERON:0001831	83.67	gold quality
nasal cavity epithelium	UBERON:0005384	83.38	silver quality
epithelial cell of pancreas	CL:0000083	82.14	gold quality
epithelium of nasopharynx	UBERON:0001951	81.84	silver quality
nasopharynx	UBERON:0001728	81.83	silver quality
palpebral conjunctiva	UBERON:0001812	81.62	gold quality
deltoid	UBERON:0001476	81.38	silver quality
bronchial epithelial cell	CL:0002328	81.21	gold quality
eye	UBERON:0000970	81.09	gold quality
superficial temporal artery	UBERON:0001614	81.02	silver quality
bronchus	UBERON:0002185	80.91	gold quality
pancreatic ductal cell	CL:0002079	80.86	silver quality
amniotic fluid	UBERON:0000173	79.66	gold quality
upper leg skin	UBERON:0004262	79.54	gold quality
pigmented layer of retina	UBERON:0001782	79.49	gold quality
retina	UBERON:0000966	79.48	gold quality
endothelial cell	CL:0000115	78.66	silver quality
jejunal mucosa	UBERON:0000399	77.93	gold quality
epithelium of mammary gland	UBERON:0003244	77.86	silver quality
mammary duct	UBERON:0001765	77.78	silver quality
cartilage tissue	UBERON:0002418	77.61	gold quality
oral cavity	UBERON:0000167	77.37	gold quality
germinal epithelium of ovary	UBERON:0001304	77.13	gold quality
skin of hip	UBERON:0001554	77.07	gold quality
cardia of stomach	UBERON:0001162	76.86	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	4.07
E-MTAB-6379	no	7.01
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting SFT2D3, 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-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-4267	99.96	66.53	2368
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sft2d3	ENSDARG00000070284
mus_musculus	Sft2d3	ENSMUSG00000044982
rattus_norvegicus	Sft2d3	ENSRNOG00000016216
caenorhabditis_elegans		WBGENE00007690

Paralogs (2): SFT2D1 (ENSG00000198818), SFT2D2 (ENSG00000213064)

Protein

Protein identifiers

Vesicle transport protein SFT2C — Q587I9 (reviewed: Q587I9)

Alternative names: SFT2 domain-containing protein 3

All UniProt accessions (1): Q587I9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex.

Subcellular location. Membrane.

Similarity. Belongs to the SFT2 family.

RefSeq proteins (1): NP_116129* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007305	Vesicle_transpt_Got1/SFT2	Family
IPR011691	Vesicle_transpt_SFT2	Family

Pfam: PF04178

UniProt features (11 total): topological domain 5, transmembrane region 4, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q587I9-F1	57.29	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, CHANDRAN_METASTASIS_DN, TERAMOTO_OPN_TARGETS_CLUSTER_5, chr2q14, GRADE_COLON_AND_RECTAL_CANCER_UP, MODULE_69, MODULE_139, MARTENS_TRETINOIN_RESPONSE_DN, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, MODULE_37, ZWANG_EGF_INTERVAL_DN, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_2H_DN, ARID5B_TARGET_GENES, ELF2_TARGET_GENES, GTF2E2_TARGET_GENES

GO Biological Process (2): protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (0):

GO Cellular Component (3): cytoplasm (GO:0005737), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
transport	2
intracellular protein localization	1
establishment of protein localization	1
cellular process	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

408 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SFT2D3	SFT2D1	Q8WV19	517
SFT2D3	ZNF668	Q96K58	471
SFT2D3	STX5	Q13190	443
SFT2D3	MAEL	Q96JY0	431
SFT2D3	ADHFE1	Q8IWW8	402
SFT2D3	CCDC116	Q8IYX3	384
SFT2D3	BOLL	Q8N9W6	373
SFT2D3	SFT2D2	O95562	370
SFT2D3	CD320	Q9NPF0	370
SFT2D3	ZC3H15	Q8WU90	368
SFT2D3	GOSR1	O95249	366
SFT2D3	SLC6A15	Q9H2J7	359
SFT2D3	LMBR1L	Q6UX01	359
SFT2D3	METTL22	Q9BUU2	353
SFT2D3	ODAPH	Q17RF5	350

IntAct

16 interactions, top by confidence:

A	B	Type	Score
GOSR2	BET1	psi-mi:“MI:0914”(association)	0.810
STX5	GOSR2	psi-mi:“MI:0914”(association)	0.670
SFT2D3	RABAC1	psi-mi:“MI:0915”(physical association)	0.400
	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
GORASP2	PGRMC1	psi-mi:“MI:0914”(association)	0.350
RAB1B	TOMM40	psi-mi:“MI:0914”(association)	0.350
RAB2A	TOMM40	psi-mi:“MI:0914”(association)	0.350
TMEM147	RPL22	psi-mi:“MI:0914”(association)	0.350
VAMP3	SCAMP1	psi-mi:“MI:0914”(association)	0.350
YIPF5	EI24	psi-mi:“MI:0914”(association)	0.350
IFITM3	PRAF2	psi-mi:“MI:0914”(association)	0.350
SLC3A1	ILVBL	psi-mi:“MI:0914”(association)	0.350
SLC5A7	FUT4	psi-mi:“MI:0914”(association)	0.350
SLC7A4	ESYT2	psi-mi:“MI:0914”(association)	0.350
TMEM216	GPR89A	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (39): SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS), SFT2D3 (Proximity Label-MS)

ESM2 similar proteins: A4IFG4, A6NH11, A6YCJ2, A8J1V4, O75064, O77751, O88941, O94766, P0C5W1, P70345, Q08DM2, Q0VD38, Q13488, Q1KZG0, Q1RMX3, Q2TBW5, Q3MHZ1, Q3U0S6, Q45T69, Q4VYA0, Q587I9, Q5JR98, Q5RE82, Q5U651, Q6GQT5, Q6PEY1, Q6UX98, Q6Z0Q9, Q80UM7, Q8BGX2, Q8BVG8, Q8C052, Q8IXM6, Q8IZY2, Q8N144, Q8N4L1, Q8VIM9, Q8WUY8, Q90343, Q90ZN1

Diamond homologs: P38166, Q587I9, Q9CSV6, Q9P6K1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
endoplasmic reticulum to Golgi vesicle-mediated transport	5	29.5×	7e-05
protein transport	6	11.4×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

104 predictions. Top by Δscore:

Variant	Effect	Δscore
2:127702890:TC:T	acceptor_gain	0.9400
2:127702891:CC:C	acceptor_gain	0.9400
2:127702892:C:CC	acceptor_gain	0.9300
2:127704794:T:TA	donor_gain	0.9300
2:127702888:AATCC:A	acceptor_loss	0.9200
2:127702891:CCT:C	acceptor_loss	0.9200
2:127702892:CTGCA:C	acceptor_loss	0.9200
2:127702893:T:A	acceptor_loss	0.9200
2:127702894:G:C	acceptor_loss	0.8900
2:127702889:ATC:A	acceptor_gain	0.8600
2:127702888:AATC:A	acceptor_gain	0.8500
2:127702895:CAAA:C	acceptor_loss	0.7700
2:127701681:G:GT	donor_gain	0.7600
2:127701574:A:T	donor_gain	0.7300
2:127702887:AAATC:A	acceptor_gain	0.7300
2:127704745:AT:A	donor_gain	0.7300
2:127701555:G:GT	donor_gain	0.6800
2:127704766:ATG:A	donor_gain	0.6700
2:127701625:G:GT	donor_gain	0.6600
2:127701652:G:GT	donor_gain	0.6600
2:127701651:G:GT	donor_gain	0.6300
2:127702895:C:CT	acceptor_gain	0.6200
2:127704795:C:A	donor_gain	0.5900
2:127704768:G:A	donor_gain	0.5800
2:127701555:GGA:G	donor_gain	0.5700
2:127701556:GAG:G	donor_gain	0.5700
2:127701893:G:GT	donor_gain	0.5700
2:127701846:C:T	donor_gain	0.5500
2:127701649:G:GT	donor_gain	0.5400
2:127702898:A:C	acceptor_gain	0.5300

AlphaMissense

1290 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:127701850:T:C	F108L	0.975
2:127701852:C:A	F108L	0.975
2:127701852:C:G	F108L	0.975
2:127701862:T:A	W112R	0.972
2:127701862:T:C	W112R	0.972
2:127701796:T:C	C90R	0.955
2:127701872:G:A	G115D	0.951
2:127701871:G:C	G115R	0.944
2:127701995:C:A	T156K	0.944
2:127701802:G:C	G92R	0.937
2:127701775:T:C	C83R	0.935
2:127701851:T:G	F108C	0.932
2:127701849:G:C	K107N	0.927
2:127701849:G:T	K107N	0.927
2:127701854:C:A	A109E	0.927
2:127701799:T:C	F91L	0.926
2:127701801:C:A	F91L	0.926
2:127701801:C:G	F91L	0.926
2:127702043:G:A	G172D	0.925
2:127702042:G:C	G172R	0.922
2:127702034:C:A	T169K	0.921
2:127701851:T:C	F108S	0.920
2:127701809:C:A	A94D	0.917
2:127701884:C:A	A119E	0.910
2:127701803:G:A	G92D	0.908
2:127702004:C:A	A159D	0.907
2:127701872:G:T	G115V	0.902
2:127702021:A:C	S165R	0.901
2:127702023:C:A	S165R	0.901
2:127702023:C:G	S165R	0.901

dbSNP variants (sampled 300 via entrez): RS1000223586 (2:127699533 G>A), RS1000970695 (2:127702842 A>C,G), RS1001003241 (2:127703143 G>A), RS1001522379 (2:127703858 C>A), RS1002644080 (2:127704311 A>G), RS1003647794 (2:127703130 T>G), RS1003940997 (2:127701738 C>T), RS1003992880 (2:127699647 T>C), RS1004022264 (2:127700003 G>A), RS1004461760 (2:127702237 G>C), RS1004930475 (2:127703853 C>T), RS1005688538 (2:127703170 G>A), RS1005936454 (2:127702351 T>C), RS1006567810 (2:127703643 G>A,C), RS1007332615 (2:127701895 A>C)

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

2 associations (top):

Study	Trait	p-value
GCST005196_206	Coronary artery disease	4.000000e-06
GCST008526_77	Coffee consumption	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006781	coffee consumption measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, decreases methylation	2
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	decreases expression	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Bortezomib	decreases expression	1
Sunitinib	increases expression	1
Acetaldehyde	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Lead	affects expression	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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