SDF2

Summary

SDF2 (stromal cell derived factor 2, HGNC:10675) is a protein-coding gene on chromosome 17q11.2, encoding Stromal cell-derived factor 2 (Q99470).

The protein encoded by this gene is believed to be a secretory protein. It has regions of similarity to hydrophilic segments of yeast mannosyltransferases. Its expression is ubiquitous and the gene appears to be relatively conserved among mammals. Alternate splicing results in both coding and non-coding variants. A pseudogene of this gene is located on chromosome 15.

Source: NCBI Gene 6388 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_006923

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:10675
Approved symbol	SDF2
Name	stromal cell derived factor 2
Location	17q11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000132581
Ensembl biotype	protein_coding
OMIM	602934
Entrez	6388

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 6 protein_coding_CDS_not_defined, 4 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000247020, ENST00000585428, ENST00000585749, ENST00000587338, ENST00000587629, ENST00000587788, ENST00000588472, ENST00000589788, ENST00000591903, ENST00000592250, ENST00000893451, ENST00000893452

RefSeq mRNA: 1 — MANE Select: NM_006923 NM_006923

CCDS: CCDS11238

Canonical transcript exons

ENST00000247020 — 3 exons

Exon	Start	End
ENSE00002775827	28648346	28649276
ENSE00002804148	28661726	28661906
ENSE00003577599	28655287	28655483

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 97.29.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.0140 / max 133.3829, expressed in 1815 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
165049	11.8442	1793
165050	7.0024	1755
165048	1.1674	780

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
stromal cell of endometrium	CL:0002255	97.29	gold quality
adrenal tissue	UBERON:0018303	97.15	gold quality
islet of Langerhans	UBERON:0000006	97.09	gold quality
right adrenal gland cortex	UBERON:0035827	96.64	gold quality
right adrenal gland	UBERON:0001233	96.49	gold quality
left adrenal gland	UBERON:0001234	96.45	gold quality
left adrenal gland cortex	UBERON:0035825	96.23	gold quality
mucosa of transverse colon	UBERON:0004991	95.84	gold quality
adrenal gland	UBERON:0002369	95.63	gold quality
adenohypophysis	UBERON:0002196	95.31	gold quality
rectum	UBERON:0001052	95.28	gold quality
adrenal cortex	UBERON:0001235	95.24	gold quality
granulocyte	CL:0000094	94.85	gold quality
right ovary	UBERON:0002118	94.79	gold quality
monocyte	CL:0000576	94.59	gold quality
right lobe of thyroid gland	UBERON:0001119	94.58	gold quality
left ovary	UBERON:0002119	94.52	gold quality
leukocyte	CL:0000738	94.36	gold quality
descending thoracic aorta	UBERON:0002345	94.31	gold quality
mononuclear cell	CL:0000842	94.25	gold quality
left lobe of thyroid gland	UBERON:0001120	94.18	gold quality
endocervix	UBERON:0000458	94.09	gold quality
pancreas	UBERON:0001264	94.06	gold quality
minor salivary gland	UBERON:0001830	94.06	gold quality
gall bladder	UBERON:0002110	93.94	gold quality
apex of heart	UBERON:0002098	93.93	gold quality
thoracic aorta	UBERON:0001515	93.92	gold quality
ectocervix	UBERON:0012249	93.90	gold quality
ascending aorta	UBERON:0001496	93.87	gold quality
body of pancreas	UBERON:0001150	93.84	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.67

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AR

miRNA regulators (miRDB)

56 targeting SDF2, 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-6133	100.00	66.48	2064
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-6794-5P	99.76	66.38	1048
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4716-3P	99.69	66.73	1022
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-185-5P	99.35	68.60	2497
HSA-MIR-4644	99.35	69.12	2514
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-6731-5P	99.28	67.42	2375
HSA-MIR-8085	99.28	67.56	2362
HSA-MIR-3973	99.20	69.19	1990
HSA-MIR-6814-5P	99.03	66.68	1273
HSA-MIR-374A-3P	98.87	67.82	1531
HSA-MIR-6760-5P	98.87	66.73	1515
HSA-MIR-3149	98.77	67.13	1639
HSA-MIR-6761-5P	98.71	68.03	1504

Literature-anchored findings (GeneRIF, showing 6)

• SDF-2, SDF-4 and SDF-5 are expressed in mammary tissues and cells and that a reduced level of SDF-2 and SDF-4 are associated with a poor clinical outcome. (PMID:19513569)
• Data indicate a function for stromal cell-derived factor 2 (SDF2) as a component of the heat-shock proteins 90-endothelial nitric oxide synthase (Hsp90-eNOS) complex that is critical for signal transduction in endothelial cells. (PMID:26286023)
• Hsp72 prevented SDF-2 degradation in a chaperone activity-dependent manner avoiding oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells. (PMID:27157913)
• These findings suggest that SDF2 may be an important regulatory factor by which trophoblast cells can control cell survival under ER stress. (PMID:27335075)
• SDF2 associates with ERdj3 and acts as a component in the BiP chaperone cycle to prevent the aggregation of misfolded proteins. (PMID:28597544)
• Stromal Cell-Derived Factor (SDF) 2 and the Endoplasmic Reticulum Stress Response of Trophoblast Cells in Gestational Diabetes Mellitus and In vitro Hyperglycaemic Condition. (PMID:32504504)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	sdf2	ENSDARG00000024026
mus_musculus	Sdf2	ENSMUSG00000002064
rattus_norvegicus	Sdf2	ENSRNOG00000012121
caenorhabditis_elegans	R12E2.13	WBGENE00020038

Paralogs (3): POMT2 (ENSG00000009830), SDF2L1 (ENSG00000128228), POMT1 (ENSG00000130714)

Protein

Protein identifiers

Stromal cell-derived factor 2 — Q99470 (reviewed: Q99470)

All UniProt accessions (4): Q99470, K7ELH6, K7ELI9, Q6IBU4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

RefSeq proteins (1): NP_008854* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016093	MIR_motif	Domain
IPR036300	MIR_dom_sf	Homologous_superfamily

Pfam: PF02815

UniProt features (9 total): domain 3, sequence conflict 3, signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q99470-F1	90.65	0.82

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 126 (showing top): RNGTGGGC_UNKNOWN, KAAB_FAILED_HEART_ATRIUM_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, LHX3_01, chr17q11, GOBP_PROTEIN_MATURATION, GGAANCGGAANY_UNKNOWN, GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN, GOBP_PROTEIN_FOLDING, AACTTT_UNKNOWN, P300_01, GOBP_PROTEIN_REFOLDING, ACEVEDO_LIVER_CANCER_UP, DANG_BOUND_BY_MYC, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN

GO Biological Process (1): protein refolding (GO:0042026)

GO Molecular Function (1): misfolded protein binding (GO:0051787)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), protein folding chaperone complex (GO:0101031), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein folding	1
protein binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
intracellular protein-containing complex	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1066 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SDF2	KDELR1	P24390	848
SDF2	DNAJB11	Q9UBS4	712
SDF2	POMT1	Q9Y6A1	709
SDF2	DNAJB1	P25685	562
SDF2	HSPA5	P11021	559
SDF2	STT3A	P46977	507
SDF2	PDIA4	P13667	466
SDF2	HSP90B1	P14625	462
SDF2	UGGT2	Q9NYU1	439
SDF2	SEZ6	Q53EL9	435
SDF2	UGGT1	Q9NYU2	433
SDF2	PPIB	P23284	428
SDF2	SLC25A35	Q3KQZ1	413
SDF2	THUMPD2	Q9BTF0	412
SDF2	SPAG1	Q07617	409

IntAct

42 interactions, top by confidence:

A	B	Type	Score
	PLOD2	psi-mi:“MI:0914”(association)	0.530
ILK	ILVBL	psi-mi:“MI:0914”(association)	0.530
SDF2	ALS2	psi-mi:“MI:0914”(association)	0.530
env	PSMD11	psi-mi:“MI:0914”(association)	0.460
env	APP	psi-mi:“MI:0914”(association)	0.460
env	PGRMC1	psi-mi:“MI:0914”(association)	0.460
	AGPS	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
HSPB2	SDF2	psi-mi:“MI:0915”(physical association)	0.370
Tpm1	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
Septin9	SEPTIN8	psi-mi:“MI:0914”(association)	0.350
K1	HLA-A	psi-mi:“MI:0914”(association)	0.350
SECTM1	BCLAF1	psi-mi:“MI:0914”(association)	0.350
PSG1	IKBKB	psi-mi:“MI:0914”(association)	0.350
SDF2	HSPA5	psi-mi:“MI:0914”(association)	0.350
DMWD	P4HA2	psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
PSKH2	AIP	psi-mi:“MI:0914”(association)	0.350
INSR	HAX1	psi-mi:“MI:0914”(association)	0.350
NTRK3	ILVBL	psi-mi:“MI:0914”(association)	0.350
ROS1	ODAD3	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
SDF2	BMP1	psi-mi:“MI:0914”(association)	0.350
DNAJB11	CDC42EP1	psi-mi:“MI:0914”(association)	0.350
AFG2B	MMP24OS	psi-mi:“MI:0914”(association)	0.350

BioGRID (97): SDF2 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), SDF2 (Co-fractionation), SDF2 (Two-hybrid), SDF2 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), ALS2 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), DNAJB11 (Affinity Capture-MS), SDF2 (Affinity Capture-MS), SDF2 (Reconstituted Complex), SDF2 (Affinity Capture-MS), SDF2 (Affinity Capture-MS)

ESM2 similar proteins: F1Q8R9, O08912, P09958, P23188, P23377, P29119, P31382, P34678, Q07537, Q10471, Q10472, Q10473, Q19791, Q28193, Q29121, Q3SZ45, Q3T083, Q49A17, Q54P23, Q5RFJ6, Q60716, Q6DJR8, Q6P6V1, Q6P9S7, Q6PB93, Q6UE39, Q6WV16, Q6WV17, Q6WV19, Q80VA0, Q86SF2, Q86SR1, Q8BVG5, Q8CF93, Q8IA42, Q8IUC8, Q8MV48, Q8N428, Q8NCW6, Q91610

Diamond homologs: F1Q8R9, F1QF89, O13898, O74189, P31382, P33775, P42934, P46971, P47190, P52867, Q29IL2, Q2LZ62, Q3SZ45, Q54P23, Q59X23, Q5A688, Q5ACU3, Q5ADM9, Q8BGQ4, Q8R2R1, Q93ZE8, Q99470, Q99PR0, Q9C100, Q9DCT5, Q9UKY4, Q9VTK2, Q9W5D4, Q9Y6A1, Q3T083, Q9ESP1, Q9HCN8, O42933

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

760 predictions. Top by Δscore:

Variant	Effect	Δscore
17:28649273:CTTC:C	acceptor_gain	0.9900
17:28649276:CCTAG:C	acceptor_loss	0.9900
17:28649277:CTAG:C	acceptor_loss	0.9900
17:28649278:T:C	acceptor_loss	0.9900
17:28649277:C:CC	acceptor_gain	0.9800
17:28655281:CCTCA:C	donor_loss	0.9800
17:28655282:CTCAC:C	donor_loss	0.9800
17:28655283:TCACC:T	donor_loss	0.9800
17:28655284:CA:C	donor_loss	0.9800
17:28655285:A:AA	donor_loss	0.9800
17:28655286:C:CT	donor_loss	0.9800
17:28655480:CTAC:C	acceptor_gain	0.9800
17:28662044:A:AC	donor_gain	0.9700
17:28662045:C:CC	donor_gain	0.9700
17:28662045:CGATA:C	donor_gain	0.9600
17:28655484:C:CG	acceptor_loss	0.9500
17:28655485:T:A	acceptor_loss	0.9500
17:28649275:TC:T	acceptor_gain	0.9400
17:28649276:CC:C	acceptor_gain	0.9400
17:28655486:G:C	acceptor_loss	0.9400
17:28661722:TTA:T	donor_loss	0.9400
17:28661723:TA:T	donor_loss	0.9400
17:28661727:TG:T	donor_gain	0.9400
17:28649288:A:T	acceptor_loss	0.9200
17:28662183:G:GT	donor_gain	0.9200
17:28649279:A:C	acceptor_loss	0.9100
17:28661728:G:T	donor_gain	0.9100
17:28649287:C:CT	acceptor_loss	0.9000
17:28661742:G:C	donor_gain	0.8800
17:28661953:C:CT	acceptor_gain	0.8800

AlphaMissense

1366 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:28649228:A:G	W133R	1.000
17:28649228:A:T	W133R	1.000
17:28649262:A:C	F121L	1.000
17:28649262:A:T	F121L	1.000
17:28649264:A:G	F121L	1.000
17:28649268:A:C	S119R	1.000
17:28649268:A:T	S119R	1.000
17:28649270:T:G	S119R	1.000
17:28655320:A:C	S105R	1.000
17:28655320:A:T	S105R	1.000
17:28655322:T:G	S105R	1.000
17:28655325:G:C	H104D	1.000
17:28655327:A:G	L103P	1.000
17:28655327:A:T	L103H	1.000
17:28655425:C:A	W70C	1.000
17:28655425:C:G	W70C	1.000
17:28655427:A:G	W70R	1.000
17:28655427:A:T	W70R	1.000
17:28649061:C:A	W188C	0.999
17:28649061:C:G	W188C	0.999
17:28649063:A:G	W188R	0.999
17:28649063:A:T	W188R	0.999
17:28649176:A:G	F150S	0.999
17:28649226:C:A	W133C	0.999
17:28649226:C:G	W133C	0.999
17:28649233:T:A	D131V	0.999
17:28649234:C:G	D131H	0.999
17:28649269:C:A	S119I	0.999
17:28649274:T:A	E117D	0.999
17:28649274:T:G	E117D	0.999

dbSNP variants (sampled 300 via entrez): RS1000191219 (17:28651229 T>A,C), RS1000726524 (17:28658198 T>C,G), RS1000797521 (17:28647850 G>A), RS1000864247 (17:28661006 T>C), RS1000977982 (17:28655557 C>A,T), RS1001027964 (17:28648594 A>G), RS1001059187 (17:28648931 A>G,T), RS1001320975 (17:28661211 T>C), RS1001352942 (17:28661456 G>A,T), RS1001405926 (17:28655799 G>A), RS1001477010 (17:28655873 T>C), RS1002014908 (17:28653261 C>T), RS1002286885 (17:28661415 A>G), RS1002304477 (17:28649365 T>C,G), RS1002335476 (17:28649565 T>C)

Disease associations

OMIM: gene MIM:602934 | 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

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, increases expression	3
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
cupric chloride	increases expression	1
ICG 001	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Vorinostat	increases expression	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cadmium	increases abundance, increases expression	1
Cisplatin	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Isoniazid	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1
Antirheumatic Agents	decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E8NN	OCUM-2M/OXA SDF2 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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