SNX20

Summary

SNX20 (sorting nexin 20, HGNC:30390) is a protein-coding gene on chromosome 16q12.1, encoding Sorting nexin-20 (Q7Z614). May play a role in cellular vesicle trafficking.

SNX20 interacts with the cytoplasmic domain of PSGL1 (SELPLG; MIM 600738) and cycles PSGL1 into endosomes.

Source: NCBI Gene 124460 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 46 total
• MANE Select transcript: NM_182854

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30390
Approved symbol	SNX20
Name	sorting nexin 20
Location	16q12.1
Locus type	gene with protein product
Status	Approved
Aliases	SLIC-1, SLIC1
Ensembl gene	ENSG00000167208
Ensembl biotype	protein_coding
OMIM	613281
Entrez	124460

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 nonsense_mediated_decay

ENST00000300590, ENST00000330943, ENST00000423026, ENST00000568993, ENST00000890682, ENST00000890683

RefSeq mRNA: 3 — MANE Select: NM_182854 NM_001144972, NM_153337, NM_182854

CCDS: CCDS10744, CCDS10745, CCDS45481

Canonical transcript exons

ENST00000330943 — 4 exons

Exon	Start	End
ENSE00001126059	50677397	50677535
ENSE00001141621	50675770	50675921
ENSE00001336654	50671629	50674074
ENSE00001357212	50681190	50681312

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 96.03.

FANTOM5 (CAGE): breadth broad, TPM avg 8.7437 / max 529.3924, expressed in 423 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
157324	5.5151	399
157323	3.0496	304
157322	0.1377	53
157326	0.0413	25

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	96.03	gold quality
blood	UBERON:0000178	94.30	gold quality
leukocyte	CL:0000738	92.79	gold quality
monocyte	CL:0000576	92.45	gold quality
vermiform appendix	UBERON:0001154	88.89	gold quality
lymph node	UBERON:0000029	88.56	gold quality
bone marrow	UBERON:0002371	88.14	gold quality
thymus	UBERON:0002370	87.01	gold quality
bone marrow cell	CL:0002092	86.55	gold quality
spleen	UBERON:0002106	85.33	gold quality
epithelium of nasopharynx	UBERON:0001951	83.32	gold quality
ileal mucosa	UBERON:0000331	83.03	gold quality
caecum	UBERON:0001153	82.87	gold quality
trabecular bone tissue	UBERON:0002483	81.68	gold quality
vastus lateralis	UBERON:0001379	79.10	gold quality
quadriceps femoris	UBERON:0001377	78.85	gold quality
biceps brachii	UBERON:0001507	78.15	gold quality
amniotic fluid	UBERON:0000173	77.86	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	77.16	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.81	gold quality
hindlimb stylopod muscle	UBERON:0004252	76.36	gold quality
tonsil	UBERON:0002372	76.12	gold quality
deltoid	UBERON:0001476	75.49	gold quality
buccal mucosa cell	CL:0002336	74.99	silver quality
skeletal muscle tissue	UBERON:0001134	74.97	gold quality
palpebral conjunctiva	UBERON:0001812	74.71	gold quality
upper arm skin	UBERON:0004263	74.63	gold quality
lower lobe of lung	UBERON:0008949	74.19	gold quality
epithelial cell of pancreas	CL:0000083	73.68	silver quality
gall bladder	UBERON:0002110	73.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

82 targeting SNX20, 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-7110-3P	100.00	73.18	2486
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-576-5P	99.84	70.46	2582
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-26A-5P	99.78	73.52	2303
HSA-MIR-26B-5P	99.78	73.51	2305
HSA-MIR-498-5P	99.76	69.64	1807
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4465	99.71	72.56	2096
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-18A-3P	99.56	65.68	1092
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-3191-3P	99.45	63.94	356
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-6731-5P	99.28	67.42	2375

Literature-anchored findings (GeneRIF, showing 3)

• Serves as a sorting molecule that cycles P-selectin ligand protein into endosomes with no impact on leukocyte recruitment. (PMID:18196517)
• Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma. (PMID:34743576)
• DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression. (PMID:35771139)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	snx20	ENSDARG00000045554
mus_musculus	Snx20	ENSMUSG00000031662
rattus_norvegicus	Snx20	ENSRNOG00000014202
drosophila_melanogaster	Snx21	FBGN0031457

Paralogs (1): SNX21 (ENSG00000124104)

Protein

Protein identifiers

Sorting nexin-20 — Q7Z614 (reviewed: Q7Z614)

Alternative names: Selectin ligand-interactor cytoplasmic 1

All UniProt accessions (1): Q7Z614

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cellular vesicle trafficking. Has been proposed to function as a sorting protein that targets SELPLG into endosomes, but has no effect on SELPLG internalization from the cell surface, or on SELPLG-mediated cell-cell adhesion.

Subunit / interactions. Interacts with SELPLG. Interaction with SELPLG is controversial.

Subcellular location. Early endosome membrane. Cell membrane. Cytoplasm. Nucleus.

Domain organisation. The PX domain binds phosphatidylinositol 3-phosphate which is necessary for localization to the endosomes.

Similarity. Belongs to the sorting nexin family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q7Z614-1	1	yes
Q7Z614-2	2
Q7Z614-3	3
Q7Z614-4	4

RefSeq proteins (3): NP_001138444, NP_699168, NP_878274* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR036871	PX_dom_sf	Homologous_superfamily
IPR039937	SNX20/SNX21	Family

Pfam: PF00787

UniProt features (15 total): splice variant 5, binding site 4, chain 1, domain 1, sequence variant 1, mutagenesis site 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z614-F1	83.76	0.64

Functional residue map

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

Ligand- & substrate-binding residues (4): 116; 118; 143; 157

Post-translational modifications (1): 3

Mutagenesis-validated functional residues (1):

Position	Phenotype
116	decreased binding activity to all phospholipids.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 129 (showing top): SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, RYTTCCTG_ETS2_B, GATA4_Q3, GOCC_EARLY_ENDOSOME_MEMBRANE, GOMF_PHOSPHATIDYLINOSITOL_4_5_BISPHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_PHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BISPHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_3_PHOSPHATE_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, CHEN_METABOLIC_SYNDROM_NETWORK, MARTENS_BOUND_BY_PML_RARA_FUSION, LEE_DIFFERENTIATING_T_LYMPHOCYTE, WARTERS_RESPONSE_TO_IR_SKIN

GO Biological Process (1): protein transport (GO:0015031)

GO Molecular Function (6): phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), phosphatidylinositol-3-phosphate binding (GO:0032266), phosphatidylinositol phosphate binding (GO:1901981), protein binding (GO:0005515), lipid binding (GO:0008289), phosphatidylinositol binding (GO:0035091)

GO Cellular Component (7): nucleoplasm (GO:0005654), plasma membrane (GO:0005886), early endosome membrane (GO:0031901), nucleus (GO:0005634), cytoplasm (GO:0005737), endosome (GO:0005768), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
phosphatidylinositol phosphate binding	2
binding	2
transport	1
intracellular protein localization	1
establishment of protein localization	1
phosphatidylinositol bisphosphate binding	1
phospholipid binding	1
anion binding	1
nuclear lumen	1
membrane	1
cell periphery	1
early endosome	1
endosome membrane	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
endomembrane system	1
cytoplasmic vesicle	1

Protein interactions and networks

STRING

762 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNX20	HECA	Q9UBI9	848
SNX20	SELPLG	Q14242	831
SNX20	FUT7	Q11130	656
SNX20	SELP	P16109	575
SNX20	CYLD	Q9NQC7	560
SNX20	SNX16	P57768	540
SNX20	NKD1	Q969G9	531
SNX20	SNX24	Q9Y343	515
SNX20	RSPRY1	Q96DX4	499
SNX20	SELE	P16111	496
SNX20	SNX10	Q9Y5X0	478
SNX20	SNX25	Q9H3E2	476
SNX20	SNX17	Q15036	470
SNX20	METTL6	Q8TCB7	466
SNX20	EAF1	Q96JC9	464

IntAct

32 interactions, top by confidence:

A	B	Type	Score
SNX20	KLHL12	psi-mi:“MI:0915”(physical association)	0.670
FAM9B	SNX20	psi-mi:“MI:0915”(physical association)	0.670
SNX20	TFIP11	psi-mi:“MI:0915”(physical association)	0.670
KLHL12	SNX20	psi-mi:“MI:0915”(physical association)	0.670
SNX20	FAM9B	psi-mi:“MI:0915”(physical association)	0.670
TFIP11	SNX20	psi-mi:“MI:0915”(physical association)	0.670
SELPLG	SNX20	psi-mi:“MI:0915”(physical association)	0.610
SELPLG	SNX20	psi-mi:“MI:0407”(direct interaction)	0.610
SNX20	SELPLG	psi-mi:“MI:0403”(colocalization)	0.610
SNX20	ALAS1	psi-mi:“MI:0915”(physical association)	0.560
MAGEA11	SNX20	psi-mi:“MI:0915”(physical association)	0.560
FLJ13057	SNX20	psi-mi:“MI:0915”(physical association)	0.560
TACC3	SNX20	psi-mi:“MI:0915”(physical association)	0.560
ALAS1	SNX20	psi-mi:“MI:0915”(physical association)	0.560
SNX20	TACC3	psi-mi:“MI:0915”(physical association)	0.560
MAGEA11	SNX20	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (31): SNX20 (Two-hybrid), SNX20 (Two-hybrid), SNX20 (Two-hybrid), SNX20 (Two-hybrid), SNX20 (Two-hybrid), SNX20 (Two-hybrid), FAM9B (Two-hybrid), SNX20 (Two-hybrid), SNX20 (Two-hybrid), JMJD4 (Affinity Capture-MS), DIRAS1 (Affinity Capture-MS), HCCS (Affinity Capture-MS), VPS13B (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), ENOSF1 (Affinity Capture-MS)

ESM2 similar proteins: A0JN53, A6NE52, A7E3N7, A8MYJ7, D3ZVB0, D4A615, E1BD59, G3MZC5, O15287, O43299, O75064, O94812, P58660, P60330, Q0P5G1, Q14674, Q1JPD6, Q2VPB7, Q3HNM7, Q3TAP4, Q3U829, Q58EX7, Q5BK61, Q6DT37, Q6NZL6, Q6ZNJ1, Q6ZQA0, Q76MJ5, Q7Z614, Q80TE0, Q80TT2, Q80UW5, Q80VA5, Q8BGI5, Q8BUI3, Q8BYG0, Q8C0Q3, Q8C159, Q8C3R1, Q8CIE4

Diamond homologs: Q2T9W1, Q3UR97, Q5BK61, Q7Z614, Q969T3, Q9D2Y5, Q9Y343, B1AVY7, P57768, P57769, Q2KHV6, Q4FZZ1, Q54TC3, Q54WZ5, Q5R6Q7, Q5R903, Q6CUC4, Q6PHS6, Q75CC3, Q7Z7A4, Q8BHY8, Q8BX57, Q8C080, Q8CFD4, Q8IPH9, Q96L93, Q9SZ67, Q9Y5W8, Q9Y5X2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	4
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

476 predictions. Top by Δscore:

Variant	Effect	Δscore
16:50675764:GCTTA:G	donor_loss	1.0000
16:50675765:CTTA:C	donor_loss	1.0000
16:50675766:TTACC:T	donor_loss	1.0000
16:50675767:TACCA:T	donor_loss	1.0000
16:50675769:C:CG	donor_loss	1.0000
16:50675769:CCA:C	donor_gain	1.0000
16:50675792:T:A	donor_gain	1.0000
16:50675922:C:CC	acceptor_gain	1.0000
16:50677450:T:TA	donor_gain	1.0000
16:50681186:TGA:T	donor_loss	1.0000
16:50681187:GAC:G	donor_loss	1.0000
16:50681189:C:T	donor_loss	1.0000
16:50674072:CAC:C	acceptor_gain	0.9900
16:50674074:CCTAG:C	acceptor_loss	0.9900
16:50675768:A:AC	donor_gain	0.9900
16:50675769:C:CC	donor_gain	0.9900
16:50675778:TAGAG:T	donor_gain	0.9900
16:50675779:AGAGA:A	donor_gain	0.9900
16:50675917:TGTGT:T	acceptor_gain	0.9900
16:50675918:GTGT:G	acceptor_gain	0.9900
16:50675919:TGT:T	acceptor_gain	0.9900
16:50675919:TGTC:T	acceptor_loss	0.9900
16:50675920:GT:G	acceptor_gain	0.9900
16:50677382:AAG:A	donor_gain	0.9900
16:50677399:AAGTG:A	donor_gain	0.9900
16:50681188:ACCT:A	donor_gain	0.9900
16:50681189:CCT:C	donor_gain	0.9900
16:50681189:CCTC:C	donor_gain	0.9900
16:50681191:T:TA	donor_gain	0.9900
16:50674075:C:CC	acceptor_gain	0.9800

AlphaMissense

2028 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:50673998:A:G	F120S	0.997
16:50673808:G:C	F183L	0.994
16:50673808:G:T	F183L	0.994
16:50673810:A:G	F183L	0.994
16:50673809:A:G	F183S	0.993
16:50674058:A:T	V100D	0.992
16:50675819:A:G	F78S	0.992
16:50675773:A:C	F93L	0.991
16:50675773:A:T	F93L	0.991
16:50675775:A:G	F93L	0.991
16:50675818:A:C	F78L	0.990
16:50675818:A:T	F78L	0.990
16:50675820:A:G	F78L	0.990
16:50674013:C:G	R115P	0.987
16:50673436:C:A	K307N	0.986
16:50673436:C:G	K307N	0.986
16:50673997:G:C	F120L	0.986
16:50673997:G:T	F120L	0.986
16:50673998:A:C	F120C	0.986
16:50673999:A:G	F120L	0.986
16:50673888:G:T	R157S	0.985
16:50674071:A:C	Y96D	0.985
16:50673809:A:C	F183C	0.983
16:50673989:A:G	L123P	0.983
16:50673608:C:T	G250E	0.981
16:50673649:G:C	C236W	0.981
16:50673664:G:C	C231W	0.981
16:50673609:C:G	G250R	0.980
16:50673609:C:T	G250R	0.980
16:50673928:C:A	K143N	0.978

dbSNP variants (sampled 300 via entrez): RS1000381424 (16:50676712 T>C,G), RS1000632392 (16:50677807 T>A), RS1000646066 (16:50682678 C>T), RS1000656894 (16:50678059 AT>A), RS1000686688 (16:50682522 G>A,C,T), RS1001058451 (16:50666648 A>G), RS1001287824 (16:50672571 T>C), RS1001297952 (16:50675572 T>C), RS1001385819 (16:50675395 A>G), RS1001531189 (16:50669543 C>T), RS1001596281 (16:50669574 C>T), RS1001662688 (16:50680593 G>A,T), RS1001719982 (16:50681424 T>C), RS1001940983 (16:50669727 T>A), RS1002263896 (16:50679491 C>G,T)

Disease associations

OMIM: gene MIM:613281 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST001438_12	Crohn’s disease	1.000000e-37
GCST003958_1	Inflammatory bowel disease	3.000000e-24
GCST003958_13	Inflammatory bowel disease	5.000000e-13
GCST003958_9	Inflammatory bowel disease	4.000000e-22
GCST003959_1	Crohn’s disease	2.000000e-54
GCST003959_4	Crohn’s disease	6.000000e-26
GCST003959_7	Crohn’s disease	8.000000e-45
GCST004131_18	Inflammatory bowel disease	1.000000e-38
GCST004132_6	Crohn’s disease	6.000000e-99
GCST007995_1	Asthma (childhood onset)	4.000000e-08
GCST009391_476	Metabolite levels	1.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010389	phosphatidylcholine 40:6 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, increases mutagenesis	2
triphenyl phosphate	affects expression	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	increases expression	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

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