SFT2D1

Summary

SFT2D1 (SFT2 domain containing 1, HGNC:21102) is a protein-coding gene on chromosome 6q27, encoding Vesicle transport protein SFT2A (Q8WV19). 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 113402 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 43 total — 1 pathogenic
• MANE Select transcript: NM_145169

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21102
Approved symbol	SFT2D1
Name	SFT2 domain containing 1
Location	6q27
Locus type	gene with protein product
Status	Approved
Aliases	MGC19825, pRGR1
Ensembl gene	ENSG00000198818
Ensembl biotype	protein_coding
Entrez	113402

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 5 protein_coding_CDS_not_defined

ENST00000361731, ENST00000478705, ENST00000479490, ENST00000487841, ENST00000488773, ENST00000494682, ENST00000866111, ENST00000921766, ENST00000921767, ENST00000921768

RefSeq mRNA: 1 — MANE Select: NM_145169 NM_145169

CCDS: CCDS5292

Canonical transcript exons

ENST00000361731 — 8 exons

Exon	Start	End
ENSE00001948203	166319728	166320256
ENSE00001952597	166342419	166342545
ENSE00003470850	166324537	166324595
ENSE00003502820	166330161	166330247
ENSE00003588646	166329507	166329589
ENSE00003602120	166328276	166328357
ENSE00003663797	166326132	166326167
ENSE00003689071	166322857	166322886

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 41.7977 / max 767.3723, expressed in 1820 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
76674	41.3692	1820
76675	0.4285	221

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
epithelial cell of pancreas	CL:0000083	98.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.20	gold quality
spinal cord	UBERON:0002240	98.11	gold quality
ileal mucosa	UBERON:0000331	98.04	gold quality
tibia	UBERON:0000979	97.72	gold quality
palpebral conjunctiva	UBERON:0001812	97.58	gold quality
esophagus squamous epithelium	UBERON:0006920	97.41	gold quality
mucosa of sigmoid colon	UBERON:0004993	97.35	gold quality
parotid gland	UBERON:0001831	97.28	gold quality
epithelium of nasopharynx	UBERON:0001951	97.23	gold quality
colonic mucosa	UBERON:0000317	97.21	gold quality
mucosa of transverse colon	UBERON:0004991	97.13	gold quality
inferior vagus X ganglion	UBERON:0005363	97.10	gold quality
germinal epithelium of ovary	UBERON:0001304	97.09	gold quality
kidney epithelium	UBERON:0004819	97.05	gold quality
monocyte	CL:0000576	96.96	gold quality
body of pancreas	UBERON:0001150	96.96	gold quality
leukocyte	CL:0000738	96.77	gold quality
thymus	UBERON:0002370	96.52	gold quality
rectum	UBERON:0001052	96.51	gold quality
saliva-secreting gland	UBERON:0001044	96.49	gold quality
pylorus	UBERON:0001166	96.42	gold quality
corpus callosum	UBERON:0002336	96.42	gold quality
lymph node	UBERON:0000029	96.40	gold quality
substantia nigra	UBERON:0002038	96.38	gold quality
pons	UBERON:0000988	96.31	gold quality
amygdala	UBERON:0001876	96.31	gold quality
hypothalamus	UBERON:0001898	96.30	gold quality
duodenum	UBERON:0002114	96.29	gold quality
caudate nucleus	UBERON:0001873	96.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

75 targeting SFT2D1, 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-656-3P	100.00	72.15	2788
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-126-5P	100.00	72.71	3180
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-2110	99.96	66.68	1930
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-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
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

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	sft2d1	ENSDARG00000007362
mus_musculus	Sft2d1rt	ENSMUSG00000069899
mus_musculus	Sft2d1	ENSMUSG00000073468
rattus_norvegicus	Sft2d1	ENSRNOG00000024140
drosophila_melanogaster	CG5104	FBGN0037009
caenorhabditis_elegans	F27D4.7	WBGENE00009191

Paralogs (2): SFT2D3 (ENSG00000173349), SFT2D2 (ENSG00000213064)

Protein

Protein identifiers

Vesicle transport protein SFT2A — Q8WV19 (reviewed: Q8WV19)

Alternative names: SFT2 domain-containing protein 1, pRGR1

All UniProt accessions (1): Q8WV19

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_660152* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007305	Vesicle_transpt_Got1/SFT2	Family
IPR011691	Vesicle_transpt_SFT2	Family

Pfam: PF04178

UniProt features (13 total): topological domain 5, transmembrane region 4, chain 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WV19-F1	74.35	0.00

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 (1): 9

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 135 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN, chr6q27, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS, ELF2_TARGET_GENES, FOXN3_TARGET_GENES, HMGA1_TARGET_GENES, NFKBIA_TARGET_GENES, SETD7_TARGET_GENES, ZNF30_TARGET_GENES, ZNF407_TARGET_GENES, MIR607, MIR548E_5P, MIR548P, MIR23A_3P_MIR23B_3P

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

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

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
binding	1
intracellular anatomical structure	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

598 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SFT2D1	PRR18	Q8N4B5	652
SFT2D1	C6orf118	Q5T5N4	593
SFT2D1	RPS6KA2	Q15349	554
SFT2D1	SFT2D3	Q587I9	517
SFT2D1	CTDNEP1	O95476	497
SFT2D1	FAM43A	Q8N2R8	489
SFT2D1	UNC93A	Q86WB7	447
SFT2D1	MAL2	Q969L2	443
SFT2D1	PABIR3	Q6P4D5	434
SFT2D1	B9ZVM9	B9ZVM9	419
SFT2D1	FRMD1	Q8N878	418
SFT2D1	KIF25	Q9UIL4	418
SFT2D1	MFSD6	Q6ZSS7	417
SFT2D1	P4HA1	P13674	394
SFT2D1	J3KPS3	J3KPS3	387

IntAct

96 interactions, top by confidence:

A	B	Type	Score
TARS2	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
NDRG4	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
MST1	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
EHHADH	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	TMEM14B	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	SLC10A1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	TARS2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	NDRG4	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	MYG1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	DERL2	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	PLEKHB2	psi-mi:“MI:0915”(physical association)	0.560
SLC30A8	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
STOM	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
ARFIP1	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
TMEM255B	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	PNKP	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	OTULIN	psi-mi:“MI:0915”(physical association)	0.560
AQP6	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	SPG21	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	MIEF2	psi-mi:“MI:0915”(physical association)	0.560
TMEM86B	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560
SFT2D1	SCN3B	psi-mi:“MI:0915”(physical association)	0.560
SCAND1	SFT2D1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (43): SFT2D1 (Proximity Label-MS), SFT2D1 (Proximity Label-MS), SFT2D1 (Proximity Label-MS), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (Two-hybrid), SFT2D1 (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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	18
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527321	GRCh37/hg19 6q26-27(chr6:162381975-170919482)	Pathogenic

SpliceAI

1687 predictions. Top by Δscore:

Variant	Effect	Δscore
6:166328270:ACTT:A	donor_loss	1.0000
6:166328271:CT:C	donor_loss	1.0000
6:166328272:TTAC:T	donor_loss	1.0000
6:166328274:A:AC	donor_gain	1.0000
6:166328274:A:T	donor_loss	1.0000
6:166328274:ACAAG:A	donor_gain	1.0000
6:166328275:C:CC	donor_gain	1.0000
6:166328275:CA:C	donor_gain	1.0000
6:166328275:CAA:C	donor_gain	1.0000
6:166328275:CAAG:C	donor_gain	1.0000
6:166328275:CAAGC:C	donor_gain	1.0000
6:166328353:ATGTA:A	acceptor_gain	1.0000
6:166328354:TGTA:T	acceptor_gain	1.0000
6:166328355:GTA:G	acceptor_gain	1.0000
6:166328356:TA:T	acceptor_gain	1.0000
6:166328358:C:CC	acceptor_gain	1.0000
6:166329588:CC:C	acceptor_gain	1.0000
6:166329589:CC:C	acceptor_gain	1.0000
6:166330155:A:C	donor_gain	1.0000
6:166330159:A:AC	donor_gain	1.0000
6:166330160:C:CC	donor_gain	1.0000
6:166342413:CGCTA:C	donor_loss	1.0000
6:166342414:GCTAC:G	donor_loss	1.0000
6:166342415:CTACC:C	donor_loss	1.0000
6:166342416:TACC:T	donor_loss	1.0000
6:166342417:A:C	donor_loss	1.0000
6:166342418:CCT:C	donor_loss	1.0000
6:166320222:T:C	acceptor_gain	0.9900
6:166320256:CCTGG:C	acceptor_gain	0.9900
6:166324596:C:CC	acceptor_gain	0.9900

AlphaMissense

1025 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:166322880:G:C	S139R	0.999
6:166322880:G:T	S139R	0.999
6:166322882:T:G	S139R	0.999
6:166324538:A:G	W137R	0.998
6:166324538:A:T	W137R	0.998
6:166328300:T:A	R97S	0.998
6:166328300:T:G	R97S	0.998
6:166328301:C:G	R97T	0.998
6:166328346:A:G	L82S	0.998
6:166329528:C:A	G71V	0.998
6:166329528:C:T	G71D	0.998
6:166329529:C:G	G71R	0.998
6:166322885:A:G	Y138H	0.997
6:166326164:A:G	C107R	0.997
6:166328301:C:A	R97I	0.997
6:166328341:C:G	G84R	0.997
6:166328341:C:T	G84R	0.997
6:166329507:C:A	S78I	0.997
6:166329588:C:T	G51E	0.997
6:166329589:C:G	G51R	0.997
6:166329589:C:T	G51R	0.997
6:166330180:C:T	G44D	0.997
6:166330181:C:G	G44R	0.997
6:166330200:A:C	F37L	0.997
6:166330200:A:T	F37L	0.997
6:166330202:A:G	F37L	0.997
6:166322869:A:T	I143N	0.996
6:166328289:G:T	T101K	0.996
6:166328340:C:T	G84E	0.996
6:166328357:A:C	S78R	0.996

dbSNP variants (sampled 300 via entrez): RS1000106944 (6:166327346 C>T), RS1000221317 (6:166327119 G>A), RS1000250935 (6:166326911 T>C), RS1000274571 (6:166333181 C>G), RS1000306496 (6:166340479 C>T), RS1000337212 (6:166340131 T>C), RS1000836511 (6:166337068 G>A), RS1000950783 (6:166336736 ATTT>A), RS1001018963 (6:166342565 A>C,G,T), RS1001021894 (6:166323000 T>C), RS1001156494 (6:166328110 T>G), RS1001167473 (6:166333363 C>T), RS1001197558 (6:166321138 GT>G,GTT), RS1001221758 (6:166339774 C>T), RS1001253013 (6:166339418 T>A,C,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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, affects expression, increases abundance, decreases expression	2
ginger extract	affects cotreatment, affects expression, increases abundance	1
dicrotophos	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
chloropicrin	increases expression	1
bisphenol S	decreases methylation	1
jinfukang	decreases expression	1
Sunitinib	increases expression	1
Air Pollutants, Occupational	decreases expression	1
Bile Acids and Salts	increases expression	1
Carbamazepine	affects expression	1
Dimethyl Sulfoxide	increases expression	1
Nickel	decreases expression	1
Oils, Volatile	affects cotreatment, affects expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	affects expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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