SNX21

Summary

SNX21 (sorting nexin family member 21, HGNC:16154) is a protein-coding gene on chromosome 20q13.12, encoding Sorting nexin-21 (Q969T3). Binds to membranes enriched in phosphatidylinositol 3-phosphate (PtdIns(P3)) and phosphatidylinositol 4,5-bisphosphate.

This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members. The specific function of this protein has not been determined. Multiple transcript variants encoding distinct isoforms have been identified for this gene.

Source: NCBI Gene 90203 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 71 total
• GTEx eGene: eQTL in 32 tissues, sQTL in 28 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.70 (unconstrained)
• MANE Select transcript: NM_033421
• Notable: 71 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16154
Approved symbol	SNX21
Name	sorting nexin family member 21
Location	20q13.12
Locus type	gene with protein product
Status	Approved
Aliases	dJ337O18.4, SNX-L
Ensembl gene	ENSG00000124104
Ensembl biotype	protein_coding
OMIM	619200
Entrez	90203

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 11 protein_coding, 5 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

MANE Select: ENST00000491381

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 5, TSL 2: 3, TSL 3: 4, TSL 5: 1

ENST00000491381, ENST00000342644, ENST00000344780, ENST00000372541, ENST00000372542, ENST00000372547, ENST00000462307, ENST00000465997, ENST00000466252, ENST00000472219, ENST00000478230, ENST00000486336, ENST00000614929, ENST00000984771, ENST00000984772, ENST00000984773, ENST00001048923, ENST00001048926, ENST00001133436

RefSeq mRNA: 4 — MANE Select: NM_033421 NM_001042632, NM_001042633, NM_033421, NM_152897

CCDS: CCDS13376, CCDS13377, CCDS42883

Canonical transcript exons

ENST00000491381 — 4 exons

Exon	Start	End
ENSE00003620951	45834959	45835116
ENSE00003633033	45834201	45834468
ENSE00003844486	45840639	45843276
ENSE00003848971	45833799	45833940

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 94.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.5379 / max 131.0502, expressed in 1649 samples.

Highest expression (Bgee): skin of leg, ovary, skin of abdomen, coronary artery, endothelial cell.

Genetic regulation across tissues (GTEx eQTL / sQTL)

SNX21 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 32 tissues and its splicing (sQTL) in 28 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 60 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Esophagus Mucosa	eqtl	9.2e-40	+0.34	20:45825016:T:C
Brain Cerebellum	eqtl	1.6e-30	-0.60	20:45826537:A:G
Brain Cerebellar Hemisphere	eqtl	1.1e-28	-0.55	20:45817461:G:A
Thyroid	eqtl	2.5e-28	+0.35	20:45840343:A:AC
Muscle Skeletal	eqtl	1.4e-23	-0.26	20:45827420:T:C
Esophagus Muscularis	eqtl	2.9e-19	+0.25	20:45850666:A:G
Nerve Tibial	sqtl	1.1e-16	+0.54	20:45847934:A:G
Whole Blood	eqtl	1.3e-16	-0.21	20:45791998:G:A
Artery Aorta	eqtl	5.0e-16	+0.28	20:45875841:T:A
Artery Tibial	sqtl	5.5e-16	-0.56	20:45839873:T:C
Colon Sigmoid	eqtl	3.2e-15	+0.33	20:45850666:A:G
Muscle Skeletal	sqtl	3.4e-15	+0.47	20:45840292:T:C
Artery Tibial	eqtl	1.5e-13	+0.25	20:45860835:G:A
Skin Sun Exposed Lower leg	sqtl	1.4e-11	+0.41	20:45860427:A:ATTGC
Nerve Tibial	eqtl	8.4e-11	+0.19	20:45847934:A:G
Skin Not Sun Exposed Suprapubic	sqtl	1.1e-09	+0.45	20:45850666:A:G
Esophagus Gastroesophageal Junction	eqtl	1.3e-09	+0.27	20:45840292:T:C
Heart Atrial Appendage	eqtl	3.8e-09	+0.29	20:45839873:T:C
Stomach	eqtl	4.4e-09	+0.19	20:45860835:G:A
Esophagus Muscularis	sqtl	7.4e-09	+0.49	20:45849475:C:CAG

FANTOM5 promoters

5 alternative TSS:

Promoter ID	TPM avg	Samples expressed
184951	6.3350	1541
184954	4.2050	1199
184953	3.4847	1270
184952	2.1676	1083
184950	1.3456	758

Top tissues by expression

showing 100 of 255 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
skin of leg	UBERON:0001511	94.49	gold quality
right ovary	UBERON:0002118	93.94	gold quality
left ovary	UBERON:0002119	93.92	gold quality
skin of abdomen	UBERON:0001416	93.67	gold quality
right coronary artery	UBERON:0001625	93.45	gold quality
endothelial cell	CL:0000115	93.42	gold quality
right adrenal gland cortex	UBERON:0035827	93.32	gold quality
zone of skin	UBERON:0000014	93.27	gold quality
mucosa of stomach	UBERON:0001199	93.27	gold quality
right adrenal gland	UBERON:0001233	93.17	gold quality
left adrenal gland cortex	UBERON:0035825	92.98	gold quality
adrenal cortex	UBERON:0001235	92.93	gold quality
left uterine tube	UBERON:0001303	92.89	gold quality
left adrenal gland	UBERON:0001234	92.68	gold quality
endocervix	UBERON:0000458	92.59	gold quality
descending thoracic aorta	UBERON:0002345	92.40	gold quality
coronary artery	UBERON:0001621	92.33	gold quality
body of uterus	UBERON:0009853	92.29	gold quality
left coronary artery	UBERON:0001626	92.24	gold quality
popliteal artery	UBERON:0002250	92.24	gold quality
tibial artery	UBERON:0007610	92.23	gold quality
aorta	UBERON:0000947	91.98	gold quality
thoracic aorta	UBERON:0001515	91.71	gold quality
ascending aorta	UBERON:0001496	91.64	gold quality
adrenal gland	UBERON:0002369	91.51	gold quality
subcutaneous adipose tissue	UBERON:0002190	91.43	gold quality
ovary	UBERON:0000992	91.36	gold quality
ectocervix	UBERON:0012249	91.25	gold quality
layer of synovial tissue	UBERON:0007616	91.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.96	gold quality
sural nerve	UBERON:0015488	90.74	gold quality
lower esophagus mucosa	UBERON:0035834	90.70	gold quality
upper arm skin	UBERON:0004263	90.40	silver quality
apex of heart	UBERON:0002098	90.36	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	90.08	gold quality
adipose tissue	UBERON:0001013	90.05	gold quality
gastrocnemius	UBERON:0001388	90.00	gold quality
muscle of leg	UBERON:0001383	89.95	gold quality
tibial nerve	UBERON:0001323	89.91	gold quality
saphenous vein	UBERON:0007318	89.89	gold quality
myometrium	UBERON:0001296	89.88	gold quality
uterine cervix	UBERON:0000002	89.60	gold quality
lower esophagus	UBERON:0013473	89.54	gold quality
lower esophagus muscularis layer	UBERON:0035833	89.54	gold quality
skin of hip	UBERON:0001554	89.26	gold quality
omental fat pad	UBERON:0010414	89.20	gold quality
peritoneum	UBERON:0002358	89.17	gold quality
adipose tissue of abdominal region	UBERON:0007808	89.13	gold quality
vastus lateralis	UBERON:0001379	88.92	gold quality
vagina	UBERON:0000996	88.85	gold quality
stromal cell of endometrium	CL:0002255	88.53	gold quality
right atrium auricular region	UBERON:0006631	88.41	gold quality
prefrontal cortex	UBERON:0000451	88.27	gold quality
cardiac atrium	UBERON:0002081	88.14	gold quality
quadriceps femoris	UBERON:0001377	88.04	gold quality
synovial joint	UBERON:0002217	87.97	gold quality
muscle layer of sigmoid colon	UBERON:0035805	87.91	gold quality
buccal mucosa cell	CL:0002336	87.55	gold quality
right frontal lobe	UBERON:0002810	87.54	gold quality
cauda epididymis	UBERON:0004360	87.21	gold quality
penis	UBERON:0000989	87.20	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.20	gold quality
anterior cingulate cortex	UBERON:0009835	87.18	gold quality
esophagus	UBERON:0001043	86.86	gold quality
right uterine tube	UBERON:0001302	86.71	gold quality
putamen	UBERON:0001874	86.62	gold quality
prostate gland	UBERON:0002367	86.58	gold quality
skeletal muscle tissue	UBERON:0001134	86.29	gold quality
heart	UBERON:0000948	86.27	gold quality
female reproductive system	UBERON:0000474	86.17	gold quality
muscle tissue	UBERON:0002385	86.16	gold quality
fallopian tube	UBERON:0003889	86.08	gold quality
parietal pleura	UBERON:0002400	86.06	gold quality
fundus of stomach	UBERON:0001160	86.02	gold quality
nipple	UBERON:0002030	86.00	gold quality
vena cava	UBERON:0004087	85.99	gold quality
caudate nucleus	UBERON:0001873	85.91	gold quality
urinary bladder	UBERON:0001255	85.89	gold quality
heart left ventricle	UBERON:0002084	85.70	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.67	gold quality
adenohypophysis	UBERON:0002196	85.61	gold quality
tendon of biceps brachii	UBERON:0008188	85.51	gold quality
frontal cortex	UBERON:0001870	85.48	gold quality
cardiac ventricle	UBERON:0002082	85.47	gold quality
smooth muscle tissue	UBERON:0001135	85.46	gold quality
amygdala	UBERON:0001876	85.45	gold quality
neocortex	UBERON:0001950	85.45	gold quality
nucleus accumbens	UBERON:0001882	85.43	gold quality
metanephros cortex	UBERON:0010533	85.26	gold quality
right lobe of thyroid gland	UBERON:0001119	85.20	gold quality
body of stomach	UBERON:0001161	85.07	gold quality
thoracic mammary gland	UBERON:0005200	85.04	gold quality
mammary gland	UBERON:0001911	85.03	gold quality
upper leg skin	UBERON:0004262	84.99	gold quality
adrenal tissue	UBERON:0018303	84.97	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	84.88	gold quality
gall bladder	UBERON:0002110	84.87	gold quality
pituitary gland	UBERON:0000007	84.82	gold quality
esophagus mucosa	UBERON:0002469	84.69	gold quality
upper lobe of left lung	UBERON:0008952	84.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.62

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Postcentral gyrus	tissue	32.1
Frontal cortex	tissue	27.6
Choroid plexus	tissue	27.0
Locus coeruleus	tissue	23.8
Skeletal muscle	tissue	21.2	low
Nucleus accumbens	tissue	20.6
Hippocampus	tissue	19.3	not detected
Olfactory bulb	tissue	18.1
Caudate putamen	tissue	17.4
Superior colliculi	tissue	16.0
Vagina	tissue	15.0	medium
Pons	tissue	14.4
Medulla oblongata	tissue	14.3
Substantia nigra	tissue	14.3
Cerebellum	tissue	14.1	high
Periaqueductal gray	tissue	13.8
Adipose tissue	tissue	13.7	not detected
Cerebral cortex	tissue	13.6	medium
Midbrain	tissue	13.6
Spinal cord	tissue	13.6
Occipital cortex	tissue	13.6
Somatosensory cortex	tissue	13.4
Basal ganglia	tissue	13.1	low
Putamen	tissue	12.8
Thalamus	tissue	12.3
Hypothalamus	tissue	12.2
Ventral forebrain	tissue	12.2
Motor cortex	tissue	12.1
Retrosplenial cortex	tissue	12.0
Hippocampal formation	tissue	11.3
Entorhinal cortex	tissue	11.3
Septum	tissue	11.3
Retrosplenial and cingulate cortex	tissue	11.2
Temporal cortex	tissue	11.0
Insular cortex	tissue	11.0
Skin 1	tissue	10.3	high
Prefrontal cortex	tissue	10.3
Amygdala	tissue	10.3
Corpus callosum	tissue	10.1
Pituitary gland	tissue	7.9
Ovary	tissue	7.4	medium
Adrenal gland	tissue	7.3	medium
Tongue	tissue	6.2
Cervix	tissue	5.3	medium
Gallbladder	tissue	4.7	medium
Prostate	tissue	4.7	medium
Seminal vesicle	tissue	4.5	high
Esophagus	tissue	4.5	medium
Endometrium 1	tissue	4.1	medium
Lung	tissue	4.0	medium
Stomach 1	tissue	3.9	high
Salivary gland	tissue	3.9	medium
Fallopian tube	tissue	3.9	medium
Colon	tissue	3.7	high
Duodenum	tissue	3.5	high
Heart muscle	tissue	3.3	medium
Parathyroid gland	tissue	3.1	medium
Kidney	tissue	3.1	high
Urinary bladder	tissue	2.7	high
Placenta	tissue	2.7	not detected

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Nucleus ambiguus (35.9), Ventral posteromedial thalamic nucleus (31.7), Nucleus rhomboideus (31.2), Nuclei of the trapezoid body (29.7), Precentral gyrus (29.7).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting SNX21 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 41 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6857-5P	99.87	65.32	985
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-1296-3P	99.72	64.04	636
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-875-3P	99.63	69.47	2548
HSA-MIR-141-5P	99.57	67.86	897
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-548G-3P	99.48	68.67	2159
HSA-MIR-4687-3P	99.48	66.41	968
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-10B-3P	99.04	66.98	988
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6760-5P	98.87	66.73	1515
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-502-5P	98.77	66.51	906
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-6728-3P	98.63	67.63	1534
HSA-MIR-2117	98.48	67.97	1307
HSA-MIR-6072	98.00	66.47	804
HSA-MIR-4638-3P	97.90	65.75	905
HSA-MIR-3936	97.64	64.47	732
HSA-MIR-5196-3P	97.57	65.98	979
HSA-MIR-6865-3P	97.54	64.67	684

Functional genomics

gnomAD constraint: pLI 1.65e-15, LOEUF 1.7, missense Z -0.166 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000491381 — one region, missense o/e 0.98.

Literature-anchored findings (GeneRIF, showing 2)

• Data suggest that human sorting nexin-L (SNX-L) may be a regulatory gene involved in receptor protein degradation during embryonic liver development. (PMID:12459172)
• The N-terminal extension of SNX21 interacts with huntingtin and recruit Htt to an endosomal population. (PMID:30072438)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	snx21	ENSDARG00000062770
mus_musculus	Snx21	ENSMUSG00000050373
drosophila_melanogaster	Snx21	FBGN0031457

Paralogs (1): SNX20 (ENSG00000167208)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1917729) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 1 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal coat appearance	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Rattus norvegicus	Q5BK61	92.0%	Diamond
Bos taurus	Q2T9W1	78.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
UBE2C	protein-coding	11065
ZSWIM3	protein-coding	140831
TNNC2	protein-coding	7125
ZSWIM1	protein-coding	90204
ACOT8	protein-coding	10005
DNTTIP1	protein-coding	116092
WFDC3	protein-coding	140686
SPATA25	protein-coding	128497
NEURL2	protein-coding	140825
PLTP	protein-coding	5360
CTSA	protein-coding	5476

Protein

Protein identifiers

Sorting nexin-21 — Q969T3 (reviewed: Q969T3)

Alternative names: Sorting nexin L

All UniProt accessions (5): A0A0S2Z632, Q05DJ0, Q5JZH3, Q5JZH4, Q969T3

UniProt curated annotations — full annotation on UniProt →

Function. Binds to membranes enriched in phosphatidylinositol 3-phosphate (PtdIns(P3)) and phosphatidylinositol 4,5-bisphosphate. May be involved in several stages of intracellular trafficking.

Subunit / interactions. Monomer.

Subcellular location. Cytoplasmic vesicle membrane. Early endosome membrane.

Tissue specificity. Highly expressed in fetus liver, but only weakly expressed in brain, skeleton muscle, smooth muscle, and cardiac muscle, kidney, and adrenal gland.

Domain organisation. The PX domain mediates specific binding to membranes enriched in phosphatidylinositol 3-phosphate (PtdIns(P3)).

Similarity. Belongs to the sorting nexin family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q969T3-1	1	yes
Q969T3-2	2
Q969T3-3	3

RefSeq proteins (4): NP_001036097, NP_001036098, NP_219489, NP_690857 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR036871	PX_dom_sf	Homologous_superfamily
IPR039937	SNX20/SNX21	Family

Pfam: PF00787

UniProt features (14 total): binding site 4, splice variant 3, compositionally biased region 3, chain 1, domain 1, sequence variant 1, region of interest 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q969T3-F1	76.37	0.53

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): vesicles; centriolar satellite

Antibody reliability (HPA): IH approved · IF approved

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)

Position	Role
171	a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)
173	a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)
198	a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)
212	a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-3-phosphate)

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 88 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, BEIER_GLIOMA_STEM_CELL_DN, AACTTT_UNKNOWN, RYTTCCTG_ETS2_B, GOCC_EARLY_ENDOSOME_MEMBRANE, GOMF_PHOSPHATIDYLINOSITOL_4_5_BISPHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_PHOSPHATE_BINDING, MODULE_13, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BISPHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_3_PHOSPHATE_BINDING, GCACTTT_MIR175P_MIR20A_MIR106A_MIR106B_MIR20B_MIR519D, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING

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 (3): early endosome membrane (GO:0031901), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

GO top-level categories

14 GO namespaces:

Category	Terms
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
early endosome	1
endosome membrane	1
vesicle membrane	1
cytoplasmic vesicle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

showing 15 of 336 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNX21	SNX29	Q8TEQ0	596
SNX21	SPATA25	Q9BR10	551
SNX21	ZSWIM1	Q9BR11	547
SNX21	SNX16	P57768	518
SNX21	SNX31	Q8N9S9	505
SNX21	WFDC10B	Q8IUB3	501
SNX21	NEURL2	Q9BR09	484
SNX21	SNX13	Q9Y5W8	480
SNX21	WFDC3	Q8IUB2	470
SNX21	HS1BP3	Q53T59	469
SNX21	SNX17	Q15036	462
SNX21	SNX11	Q9Y5W9	460
SNX21	KIF16B	Q96L93	458
SNX21	SNX12	Q9UMY4	421
SNX21	SNX3	O60493	420

IntAct

Human interaction partners of SNX21 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

6 partners by confidence:

Partner	Interaction type	MIscore	Records
LRRK1	direct interaction	0.440	1
COX6A2	physical association	0.370	1
ACOT8	association	0.350	1
PI4KA	association	0.350	1
POLR1G	association	0.350	1
RBP4	association	0.350	1

BioGRID (87 interactions; top human partners by supporting records): AMD1 (Affinity Capture-MS; 2 records), C17orf70 (Affinity Capture-MS; 2 records), CBWD1 (Affinity Capture-MS; 2 records), DDX11 (Affinity Capture-MS; 2 records), EIF2A (Affinity Capture-MS; 2 records), HEATR6 (Affinity Capture-MS; 2 records), HTT (Affinity Capture-MS; 2 records), MADD (Affinity Capture-MS; 2 records), MARCKSL1 (Affinity Capture-MS; 2 records), MELK (Affinity Capture-MS; 2 records), MKS1 (Affinity Capture-MS; 2 records), OCRL (Affinity Capture-MS; 2 records), POLA2 (Affinity Capture-MS; 2 records), POLE2 (Affinity Capture-MS; 2 records), SLC4A7 (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for SNX21: 71 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	2
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 23 predictions of 500):

Position(s)	Effect	Δscore	Sites
20:45840421	acceptor_gain	1.0000
20:45840424	acceptor_gain	1.0000
20:45840430	acceptor_gain	1.0000
20:45840637–45840638	acceptor_loss	1.0000	4
20:45834551	donor_gain	0.9900
20:45834957–45834958	acceptor_loss	0.9900	6
20:45835117–45835118	donor_loss	0.9900	5
20:45840429	acceptor_gain	0.9900
20:45840436	acceptor_gain	0.9900
20:45840637–45840638	acceptor_loss	0.9900	2

AlphaMissense

629 missense substitutions predicted likely pathogenic (of 2,385 scored), across 177 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
N203	8	0.981	0.998
F216	8	0.977	0.997
F195	8	0.976	0.997
F175	8	0.954	0.998
F238	8	0.929	0.989
F63	8	0.920	0.982
F133	8	0.899	0.980
D174	8	0.840	0.967
F239	8	0.806	0.952
F204	7	0.992	0.998
F219	7	0.952	0.990
W334	7	0.924	0.965
W263	7	0.916	0.990
S213	7	0.895	0.989
E44	7	0.836	0.920
F325	7	0.771	0.962
W119	7	0.750	0.855
E41	7	0.699	0.816
K198	6	0.993	0.998
P196	6	0.989	0.994

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	0.000507
Glioblastoma Multiforme (validation)	unfavorable	0.000934

Disease associations

OMIM: gene MIM:619200 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects cotreatment, increases abundance, increases expression	2
Valproic Acid	affects expression, decreases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
glycidyl methacrylate	decreases expression	1
beta-lapachone	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
abrine	decreases expression	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases expression, affects cotreatment, increases abundance	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Ivermectin	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Smoke	decreases expression	1
Sulindac	increases expression	1
Thimerosal	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	increases expression	1
Urethane	decreases expression	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Vitamin K 3	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.