SFT2D2

Summary

SFT2D2 (SFT2 domain containing 2, HGNC:25140) is a protein-coding gene on chromosome 1q24.2, encoding Vesicle transport protein SFT2B (O95562). 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. Located in extracellular exosome.

Source: NCBI Gene 375035 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_199344

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25140
Approved symbol	SFT2D2
Name	SFT2 domain containing 2
Location	1q24.2
Locus type	gene with protein product
Status	Approved
Aliases	UNQ512, dJ747L4.C1.2
Ensembl gene	ENSG00000213064
Ensembl biotype	protein_coding
Entrez	375035

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000271375, ENST00000367829, ENST00000471981, ENST00000630869, ENST00000873660, ENST00000873661, ENST00000873662, ENST00000873663

RefSeq mRNA: 1 — MANE Select: NM_199344 NM_199344

CCDS: CCDS1271

Canonical transcript exons

ENST00000271375 — 8 exons

Exon	Start	End
ENSE00001760428	168242501	168253021
ENSE00003465181	168231834	168231919
ENSE00003475322	168236589	168236624
ENSE00003509371	168239131	168239160
ENSE00003587539	168231514	168231600
ENSE00003664676	168236712	168236770
ENSE00003689304	168235101	168235182
ENSE00003848829	168226004	168226142

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 99.03.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.7795 / max 922.8825, expressed in 1823 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
6481	46.5083	1823
6480	1.2712	910

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.03	gold quality
esophagus squamous epithelium	UBERON:0006920	97.43	gold quality
gingiva	UBERON:0001828	96.44	gold quality
male germ cell	CL:0000015	96.28	gold quality
gingival epithelium	UBERON:0001949	96.25	gold quality
nipple	UBERON:0002030	96.18	gold quality
superficial temporal artery	UBERON:0001614	95.96	gold quality
penis	UBERON:0000989	95.77	gold quality
skin of hip	UBERON:0001554	95.69	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.69	gold quality
upper leg skin	UBERON:0004262	95.41	gold quality
visceral pleura	UBERON:0002401	95.23	gold quality
oral cavity	UBERON:0000167	95.11	gold quality
epithelium of esophagus	UBERON:0001976	94.95	gold quality
germinal epithelium of ovary	UBERON:0001304	94.77	gold quality
renal medulla	UBERON:0000362	94.70	gold quality
synovial joint	UBERON:0002217	94.67	gold quality
mammalian vulva	UBERON:0000997	94.62	gold quality
squamous epithelium	UBERON:0006914	94.62	gold quality
palpebral conjunctiva	UBERON:0001812	94.52	gold quality
lower lobe of lung	UBERON:0008949	94.24	gold quality
parotid gland	UBERON:0001831	94.20	gold quality
epithelium of nasopharynx	UBERON:0001951	94.02	gold quality
mammary duct	UBERON:0001765	93.92	gold quality
mucosa of sigmoid colon	UBERON:0004993	93.86	gold quality
parietal pleura	UBERON:0002400	93.83	gold quality
cardia of stomach	UBERON:0001162	93.59	gold quality
pylorus	UBERON:0001166	93.58	gold quality
superior surface of tongue	UBERON:0007371	93.58	gold quality
amniotic fluid	UBERON:0000173	93.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-13	yes	22.03
E-MTAB-9801	yes	8.00
E-ANND-3	yes	7.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

54 targeting SFT2D2, 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-548AN	99.97	70.91	2817
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
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-4648	99.91	67.00	710
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-4276	99.56	67.66	2514
HSA-MIR-888-3P	99.53	69.77	1057

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	sft2d2a	ENSDARG00000070746
danio_rerio	sft2d2b	ENSDARG00000071159
mus_musculus	Sft2d2	ENSMUSG00000040848
rattus_norvegicus	Sft2d2	ENSRNOG00000003038
drosophila_melanogaster	CG5104	FBGN0037009
caenorhabditis_elegans	F27D4.7	WBGENE00009191

Paralogs (2): SFT2D3 (ENSG00000173349), SFT2D1 (ENSG00000198818)

Protein

Protein identifiers

Vesicle transport protein SFT2B — O95562 (reviewed: O95562)

Alternative names: SFT2 domain-containing protein 2

All UniProt accessions (2): O95562, Q5TIH2

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_955376* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007305	Vesicle_transpt_Got1/SFT2	Family
IPR011691	Vesicle_transpt_SFT2	Family

Pfam: PF04178

UniProt features (12 total): topological domain 5, transmembrane region 4, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O95562-F1	78.49	0.38

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 1, 9

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 168 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GTGCCTT_MIR506, VANTVEER_BREAST_CANCER_ESR1_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, VERHAAK_GLIOBLASTOMA_MESENCHYMAL, LU_EZH2_TARGETS_DN, BAKKER_FOXO3_TARGETS_UP, LEE_BMP2_TARGETS_UP, HUANG_GATA2_TARGETS_UP, OISHI_CHOLANGIOMA_STEM_CELL_LIKE_UP, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP, GSE14699_NAIVE_VS_DELETIONAL_TOLERANCE_CD8_TCELL_DN, CDC5L_TARGET_GENES

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

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

GO Cellular Component (4): cytoplasm (GO:0005737), endomembrane system (GO:0012505), membrane (GO:0016020), extracellular exosome (GO:0070062)

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
binding	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1
extracellular vesicle	1

Protein interactions and networks

STRING

598 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SFT2D2	MFAP3L	O75121	582
SFT2D2	P4HTM	Q9NXG6	543
SFT2D2	NIP7	Q9Y221	540
SFT2D2	MMS22L	Q6ZRQ5	507
SFT2D2	KCNS1	Q96KK3	506
SFT2D2	ATL2	Q8NHH9	505
SFT2D2	PALM2AKAP2	Q9Y2D5	478
SFT2D2	TBC1D22B	Q9NU19	460
SFT2D2	NUP155	O75694	434
SFT2D2	HARBI1	Q96MB7	430
SFT2D2	MCM9	Q9NXL9	418
SFT2D2	INAFM1	C9JVW0	410
SFT2D2	STEAP3	Q658P3	407
SFT2D2	MFSD6	Q6ZSS7	399
SFT2D2	BBS1	Q8NFJ9	393

IntAct

85 interactions, top by confidence:

A	B	Type	Score
SFT2D2	IFNGR2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	SLC10A6	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	TMEM143	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
MOB2	SFT2D2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	HIBADH	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	INPP5K	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	ELOVL4	psi-mi:“MI:0915”(physical association)	0.560
	SFT2D2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	STOM	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	REEP4	psi-mi:“MI:0915”(physical association)	0.560
TIMM44	SFT2D2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	REEP2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	SLC30A8	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	ATP5PF	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	AQP6	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	GPR152	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	NDRG4	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	TMEM51	psi-mi:“MI:0915”(physical association)	0.560
SFT2D2	HSD17B11	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (49): SFT2D2 (Two-hybrid), SFT2D2 (Affinity Capture-MS), SFT2D2 (Affinity Capture-RNA), SFT2D2 (Two-hybrid), SFT2D2 (Proximity Label-MS), SFT2D2 (Affinity Capture-RNA), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid), SFT2D2 (Two-hybrid)

ESM2 similar proteins: A3LPS1, A4RME3, A5DEQ7, A5DSM9, A6SFL7, A6ZMD0, A7S6Y0, A7TS55, B2ALT5, B2AR67, B3M9W1, B3NDM7, B4GRI8, B4HIJ8, B4J043, B4L0H1, B4LIH0, B4MXW6, B4PD01, B4QLP9, O14223, O74375, O95562, P11022, P38166, P47111, Q03860, Q04767, Q0CSZ7, Q0JAI9, Q12116, Q4FZV2, Q54NS7, Q5APC0, Q5SSN7, Q5U3Y5, Q6BWE7, Q6CC06, Q6CMQ1, Q6FN38

Diamond homologs: O95562, Q4FZV2, Q5SSN7, Q5U3Y5, Q8VD57, Q8WV19

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1353 predictions. Top by Δscore:

Variant	Effect	Δscore
1:168226140:GAG:G	donor_gain	1.0000
1:168226141:AG:A	donor_gain	1.0000
1:168226142:GG:G	donor_gain	1.0000
1:168226143:G:GG	donor_gain	1.0000
1:168231509:TTTA:T	acceptor_loss	1.0000
1:168231511:TAG:T	acceptor_loss	1.0000
1:168231513:G:GC	acceptor_loss	1.0000
1:168231597:GCTG:G	donor_gain	1.0000
1:168231599:TGG:T	donor_loss	1.0000
1:168231600:GGTAA:G	donor_loss	1.0000
1:168231601:G:GC	donor_loss	1.0000
1:168231602:T:A	donor_loss	1.0000
1:168233991:G:GT	donor_gain	1.0000
1:168235099:A:AG	acceptor_gain	1.0000
1:168235100:G:GG	acceptor_gain	1.0000
1:168235100:GTACC:G	acceptor_gain	1.0000
1:168236710:A:AG	acceptor_gain	1.0000
1:168236711:G:GA	acceptor_gain	1.0000
1:168236711:GT:G	acceptor_gain	1.0000
1:168239158:AAGGT:A	donor_loss	1.0000
1:168239162:T:G	donor_loss	1.0000
1:168242597:GTTTT:G	donor_gain	1.0000
1:168226139:CGAG:C	donor_gain	0.9900
1:168226140:GAGG:G	donor_gain	0.9900
1:168231512:A:AG	acceptor_gain	0.9900
1:168231513:G:GG	acceptor_gain	0.9900
1:168231513:GGTT:G	acceptor_gain	0.9900
1:168231601:G:GG	donor_gain	0.9900
1:168231917:G:GT	donor_gain	0.9900
1:168231917:G:T	donor_gain	0.9900

AlphaMissense

1036 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:168231581:G:A	G44E	0.996
1:168231898:G:A	G72D	0.996
1:168239135:A:C	S140R	0.996
1:168239137:C:A	S140R	0.996
1:168239137:C:G	S140R	0.996
1:168231559:T:C	F37L	0.995
1:168231561:C:A	F37L	0.995
1:168231561:C:G	F37L	0.995
1:168236769:T:A	W138R	0.995
1:168236769:T:C	W138R	0.995
1:168231580:G:A	G44R	0.994
1:168231580:G:C	G44R	0.994
1:168231834:G:C	G51R	0.994
1:168235156:C:A	R98S	0.994
1:168231568:T:C	C40R	0.993
1:168231898:G:T	G72V	0.993
1:168236592:T:C	C108R	0.993
1:168239148:T:A	I144K	0.993
1:168231876:T:C	F65L	0.992
1:168231878:C:A	F65L	0.992
1:168231878:C:G	F65L	0.992
1:168235112:T:A	L83H	0.992
1:168239139:T:A	L141H	0.992
1:168231548:G:T	R33M	0.991
1:168231897:G:C	G72R	0.991
1:168231557:G:A	G36D	0.990
1:168231902:T:A	N73K	0.990
1:168231902:T:G	N73K	0.990
1:168235117:G:A	G85R	0.990
1:168235117:G:C	G85R	0.990

dbSNP variants (sampled 300 via entrez): RS1000003376 (1:168229651 G>A,T), RS1000014559 (1:168226337 C>A,T), RS1000069963 (1:168238890 A>C,G), RS1000091792 (1:168224009 C>A), RS1000156149 (1:168235742 G>C), RS1000284430 (1:168231719 G>A,C), RS1000391958 (1:168242173 T>C), RS1000461718 (1:168235427 T>G), RS1000603925 (1:168227848 A>G), RS1000672131 (1:168229415 C>A,G,T), RS1000672358 (1:168240493 G>A,C), RS1000678259 (1:168226525 G>T), RS1000756823 (1:168248720 G>C), RS1000763082 (1:168241826 C>T), RS1000770814 (1:168233866 G>A)

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
GCST007600_47	Alzheimer’s disease	3.000000e-06
GCST011741_65	LDL cholesterol levels in HIV infection	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	3
Nickel	increases expression	2
Cadmium Chloride	increases palmitoylation, decreases expression, decreases reaction, increases abundance	2
FR900359	decreases phosphorylation	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	affects cotreatment, increases expression	1
deoxynivalenol	decreases expression	1
sodium arsenate	increases abundance, decreases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
methacrylaldehyde	decreases expression, increases abundance, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cadmium	decreases reaction, increases abundance, increases palmitoylation	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Phenobarbital	affects expression	1
Quercetin	increases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Dronabinol	increases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1
Lactic Acid	decreases expression	1
Volatile Organic Compounds	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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