SNX10 (sorting nexin 10)

Gene

• Entrez ID: 29887
• Gene name: Sorting nexin 10
• Gene symbol: SNX10
• Synonyms (NCBI Gene): OPTB8
• Disease Acronyms (UniProt): OPTB8
• Chromosome: 7
• Chromosome location: 7p15.2
• Summary: 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs377321694	T>A,C	Pathogenic	Synonymous variant, coding sequence variant, intron variant, stop gained
rs398123011	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant
rs587777490	C>T	Pathogenic	Coding sequence variant, genic upstream transcript variant, stop gained
rs897553060	G>A	Likely-pathogenic	Missense variant, coding sequence variant
rs1353879401	C>T	Likely-pathogenic	Coding sequence variant, intron variant, stop gained

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT024587	hsa-miR-215-5p	Microarray	19074876
MIRT026783	hsa-miR-192-5p	Microarray	19074876
MIRT543820	hsa-miR-6507-5p	PAR-CLIP	21572407
MIRT103410	hsa-miR-126-5p	PAR-CLIP	21572407
MIRT543819	hsa-miR-3928-5p	PAR-CLIP	21572407
MIRT543818	hsa-miR-6806-3p	PAR-CLIP	21572407
MIRT392899	hsa-miR-27b-5p	PAR-CLIP	21572407
MIRT543817	hsa-miR-3160-5p	PAR-CLIP	21572407
MIRT543816	hsa-miR-496	PAR-CLIP	21572407
MIRT543815	hsa-miR-331-5p	PAR-CLIP	21572407
MIRT320304	hsa-miR-4795-3p	PAR-CLIP	21572407
MIRT543814	hsa-miR-127-5p	PAR-CLIP	21572407
MIRT320305	hsa-miR-6509-5p	PAR-CLIP	21572407
MIRT543813	hsa-miR-6830-3p	PAR-CLIP	21572407
MIRT497249	hsa-miR-1252-5p	PAR-CLIP	22291592
MIRT497248	hsa-miR-1301-5p	PAR-CLIP	22291592
MIRT497247	hsa-miR-6502-5p	PAR-CLIP	22291592
MIRT103433	hsa-miR-92a-3p	HITS-CLIP	22473208
MIRT103438	hsa-miR-92b-3p	HITS-CLIP	22473208
MIRT103432	hsa-miR-32-5p	HITS-CLIP	22473208
MIRT543820	hsa-miR-6507-5p	PAR-CLIP	21572407
MIRT103410	hsa-miR-126-5p	PAR-CLIP	21572407
MIRT543819	hsa-miR-3928-5p	PAR-CLIP	21572407
MIRT543818	hsa-miR-6806-3p	PAR-CLIP	21572407
MIRT392899	hsa-miR-27b-5p	PAR-CLIP	21572407
MIRT543817	hsa-miR-3160-5p	PAR-CLIP	21572407
MIRT543816	hsa-miR-496	PAR-CLIP	21572407
MIRT543815	hsa-miR-331-5p	PAR-CLIP	21572407
MIRT320304	hsa-miR-4795-3p	PAR-CLIP	21572407
MIRT543814	hsa-miR-127-5p	PAR-CLIP	21572407
MIRT320305	hsa-miR-6509-5p	PAR-CLIP	21572407
MIRT543813	hsa-miR-6830-3p	PAR-CLIP	21572407
MIRT497249	hsa-miR-1252-5p	PAR-CLIP	22291592
MIRT497248	hsa-miR-1301-5p	PAR-CLIP	22291592
MIRT497247	hsa-miR-6502-5p	PAR-CLIP	22291592
MIRT1376657	hsa-miR-1202	CLIP-seq
MIRT1376658	hsa-miR-1245	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376665	hsa-miR-2052	CLIP-seq
MIRT1376666	hsa-miR-3591-3p	CLIP-seq
MIRT1376667	hsa-miR-3972	CLIP-seq
MIRT1376668	hsa-miR-4255	CLIP-seq
MIRT1376669	hsa-miR-4422	CLIP-seq
MIRT1376670	hsa-miR-4724-5p	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376672	hsa-miR-4776-3p	CLIP-seq
MIRT1376673	hsa-miR-622	CLIP-seq
MIRT1376674	hsa-miR-3168	CLIP-seq
MIRT1376675	hsa-miR-338-5p	CLIP-seq
MIRT1376676	hsa-miR-369-3p	CLIP-seq
MIRT1376677	hsa-miR-374c	CLIP-seq
MIRT1376678	hsa-miR-4264	CLIP-seq
MIRT1376679	hsa-miR-4328	CLIP-seq
MIRT1376680	hsa-miR-4427	CLIP-seq
MIRT1376681	hsa-miR-4517	CLIP-seq
MIRT1376682	hsa-miR-4662a-3p	CLIP-seq
MIRT1376683	hsa-miR-4666-3p	CLIP-seq
MIRT1376684	hsa-miR-4680-3p	CLIP-seq
MIRT1376685	hsa-miR-4762-3p	CLIP-seq
MIRT1376686	hsa-miR-4797-3p	CLIP-seq
MIRT1376687	hsa-miR-582-5p	CLIP-seq
MIRT1376688	hsa-miR-593	CLIP-seq
MIRT1376689	hsa-miR-654-3p	CLIP-seq
MIRT1376690	hsa-miR-655	CLIP-seq
MIRT1376691	hsa-miR-656	CLIP-seq
MIRT1376692	hsa-miR-664	CLIP-seq
MIRT1376693	hsa-miR-889	CLIP-seq
MIRT1376694	hsa-miR-3684	CLIP-seq
MIRT1376695	hsa-miR-4282	CLIP-seq
MIRT1376696	hsa-miR-4698	CLIP-seq
MIRT1376697	hsa-miR-4699-3p	CLIP-seq
MIRT1376698	hsa-miR-520d-5p	CLIP-seq
MIRT1376699	hsa-miR-524-5p	CLIP-seq
MIRT1376657	hsa-miR-1202	CLIP-seq
MIRT1376700	hsa-miR-1297	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376665	hsa-miR-2052	CLIP-seq
MIRT1376701	hsa-miR-26a	CLIP-seq
MIRT1376702	hsa-miR-26b	CLIP-seq
MIRT1376703	hsa-miR-27a	CLIP-seq
MIRT1376704	hsa-miR-27b	CLIP-seq
MIRT1376705	hsa-miR-3074-3p	CLIP-seq
MIRT1376706	hsa-miR-3144-3p	CLIP-seq
MIRT1376707	hsa-miR-3200-5p	CLIP-seq
MIRT1376708	hsa-miR-3617	CLIP-seq
MIRT1376709	hsa-miR-3647-3p	CLIP-seq
MIRT1376667	hsa-miR-3972	CLIP-seq
MIRT1376668	hsa-miR-4255	CLIP-seq
MIRT1376669	hsa-miR-4422	CLIP-seq
MIRT1376710	hsa-miR-4465	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376672	hsa-miR-4776-3p	CLIP-seq
MIRT1376711	hsa-miR-513a-5p	CLIP-seq
MIRT1376712	hsa-miR-641	CLIP-seq
MIRT1376705	hsa-miR-3074-3p	CLIP-seq
MIRT2112067	hsa-miR-3163	CLIP-seq
MIRT2112068	hsa-miR-4495	CLIP-seq
MIRT2112069	hsa-miR-4668-3p	CLIP-seq
MIRT2112070	hsa-miR-500a	CLIP-seq
MIRT1376679	hsa-miR-4328	CLIP-seq
MIRT2112071	hsa-miR-4652-3p	CLIP-seq
MIRT2335296	hsa-miR-1290	CLIP-seq
MIRT1376659	hsa-miR-148a	CLIP-seq
MIRT1376660	hsa-miR-148b	CLIP-seq
MIRT1376661	hsa-miR-152	CLIP-seq
MIRT1376662	hsa-miR-1825	CLIP-seq
MIRT1376663	hsa-miR-1909	CLIP-seq
MIRT1376664	hsa-miR-202	CLIP-seq
MIRT1376703	hsa-miR-27a	CLIP-seq
MIRT1376704	hsa-miR-27b	CLIP-seq
MIRT1376682	hsa-miR-4662a-3p	CLIP-seq
MIRT1376670	hsa-miR-4724-5p	CLIP-seq
MIRT1376671	hsa-miR-4766-5p	CLIP-seq
MIRT1376711	hsa-miR-513a-5p	CLIP-seq
MIRT2335297	hsa-miR-630	CLIP-seq
MIRT2335298	hsa-miR-944	CLIP-seq
MIRT2629313	hsa-miR-1225-5p	CLIP-seq
MIRT2629314	hsa-miR-1255a	CLIP-seq
MIRT2629315	hsa-miR-1255b	CLIP-seq
MIRT2629316	hsa-miR-421	CLIP-seq
MIRT2629317	hsa-miR-4272	CLIP-seq
MIRT2629318	hsa-miR-4738-3p	CLIP-seq
MIRT2629319	hsa-miR-4802-3p	CLIP-seq
MIRT2629320	hsa-miR-490-5p	CLIP-seq
MIRT2629321	hsa-miR-555	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001696	Process	Gastric acid secretion	IEA
GO:0005515	Function	Protein binding	IPI	25416956, 32296183, 32814053
GO:0005545	Function	1-phosphatidylinositol binding	IMP	17012226
GO:0005634	Component	Nucleus	IDA	22174188
GO:0005783	Component	Endoplasmic reticulum	IDA	22174188
GO:0005813	Component	Centrosome	IDA	21844891
GO:0006886	Process	Intracellular protein transport	IEA
GO:0006897	Process	Endocytosis	IEA
GO:0007032	Process	Endosome organization	IMP	17012226
GO:0030141	Component	Secretory granule	IEA
GO:0030316	Process	Osteoclast differentiation	ISS
GO:0031313	Component	Extrinsic component of endosome membrane	IDA	17012226
GO:0035630	Process	Bone mineralization involved in bone maturation	IEA
GO:0044691	Process	Tooth eruption	IEA
GO:0045453	Process	Bone resorption	IEA
GO:0051117	Function	ATPase binding	IPI	21844891
GO:0055074	Process	Calcium ion homeostasis	IEA
GO:0060271	Process	Cilium assembly	IMP	21844891
GO:0061512	Process	Protein localization to cilium	IMP	21844891
GO:0071539	Process	Protein localization to centrosome	IMP	21844891
GO:0090651	Component	Apical cytoplasm	IEA
GO:0097178	Process	Ruffle assembly	IEA
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

Other IDs

• MIM: 614780
• HGNC: 14974
• e!Ensembl: ENSG00000086300

Protein

• UniProt ID: Q9Y5X0
• Protein name: Sorting nexin-10
• Protein function: Probable phosphoinositide-binding protein involved in protein sorting and membrane trafficking in endosomes. Plays a role in cilium biogenesis through regulation of the transport and the localization of proteins to the cilium. Required for the l
• PDB: 4ON3, 4PZG, 6KOK
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00787	PX	40 → 124	PX domain	Domain

• Sequence:

  MFPEQQKEEFVSVWVRDPRIQKEDFWHSYIDYEICIHTNSMCFTMKTSCVRRRYREFVWL
  RQRLQSNALLVQLPELPSKNLFFNMNNRQHVDQRRQGLEDFLRKVLQNALLLSDSSLHLF
  LQSHLNSEDIEACVSGQTKYSVEEAIHKFALMNRRFPEEDEEGKKENDIDYDSESSSSGL
  GHSSDDSSSHGCKVNTAPQES

• Sequence length: 201

Associated diseases

Causal
Disease term	Disease name	dbSNP ID	References
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505
Craniosynostosis	Craniosynostosis	rs104893895, rs587777006, rs587777007, rs587777008, rs587777010, rs864321680, rs864321681, rs1057517670, rs1064794325, rs1555750816, rs1599823350
Hydrocephalus	Hydrocephalus	rs387907320, rs369384363, rs387907321, rs372127610, rs770273135, rs797045095, rs797045707, rs769795916, rs781251438, rs922703465, rs376078512, rs1567043467, rs1587149916, rs1586841546
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Optic atrophy	Optic Atrophy	rs121434508, rs267607017, rs80356524, rs80356525, rs879255560, rs104893753, rs80356529, rs397515360, rs104893620, rs199476104, rs199476112, rs199476118, rs398124298, rs770066665, rs398124299, rs61750185, rs672601379, rs727504060, rs786204830, rs794727804, rs199946797, rs863224127, rs863224131, rs863224134, rs863224906, rs372054380, rs886037828, rs764791523, rs145639028, rs1057519312, rs1064794257, rs1064794656, rs1064797303, rs774265764, rs760337383, rs1553784985, rs72653786, rs1555229948, rs1555119216, rs761743852, rs1553785338, rs1020764190, rs782581701, rs1560408865, rs761460379, rs773022324, rs782740998, rs1560327427, rs80356528, rs1734162973, rs1716524583, rs1057368575
Osteopetrosis	Osteopetrosis, OSTEOPETROSIS, AUTOSOMAL RECESSIVE 8	rs786205055, rs1562370077, rs119460973, rs1554996130, rs137853149, rs751881962, rs137853150, rs137853151, rs2134438856, rs121908669, rs121908670, rs121908671, rs121908673, rs121908655, rs121908656, rs121908658, rs121908659, rs121434432, rs121434433, rs121434434, rs121434435, rs121434436, rs2137905441, rs121909072, rs863223288, rs398123011, rs387907576, rs397515539, rs267603829, rs587777490, rs139617644, rs794727287, rs573750741, rs886048594, rs777785526, rs1057517365, rs760956030, rs757788894, rs1554250938, rs367567630, rs1208311085, rs1554995350, rs1554995341, rs774308815, rs1458295257, rs1554997884, rs200851583, rs1554998061, rs758977199, rs1554999516, rs371263807, rs1475338876, rs917505107, rs1554995381, rs1554995582, rs1554995706, rs1554997818, rs1554997997, rs748659068, rs377303800, rs1554995009, rs1554999205, rs1300297240, rs1554995330, rs1385741705, rs1554995522, rs1392364437, rs749361897, rs1159666762, rs1269558164, rs1489993984, rs1439348400, rs559224144, rs1567759023, rs1567263375, rs1565156743, rs1590817956, rs1590819834, rs377215024, rs1582396088, rs1353879401, rs1590804397, rs1590819770, rs922106856, rs776436008, rs1855347940, rs761918801, rs1064794323	22499339, 23280965, 23123320
Pulmonary arterial hypertension	Pulmonary arterial hypertension, Idiopathic pulmonary arterial hypertension	rs121909288, rs137852741, rs137852742, rs137852743, rs137852744, rs137852745, rs137852746, rs137852748, rs137852749, rs137852750, rs137852751, rs137852753, rs863223423, rs863223426, rs863223424, rs863223408, rs869025366, rs876657748, rs886039506, rs886041324, rs1060502576, rs1060502581, rs1060502584, rs1085307149, rs1085307154, rs1085307157, rs1085307163, rs1085307169, rs1085307177, rs1085307180, rs1085307184, rs1085307188, rs1085307191, rs1085307203, rs1085307222, rs1085307223, rs1085307225, rs1085307229, rs1085307234, rs1085307246, rs1085307261, rs1085307267, rs576091247, rs200948870, rs1085307278, rs1085307282, rs1085307285, rs1085307290, rs1085307301, rs1085307306, rs1085307307, rs1085307308, rs1085307315, rs1085307316, rs1553509997, rs1085307324, rs1085307340, rs1085307349, rs1085307352, rs765887545, rs1085307183, rs1555208696, rs1592224412, rs1574415785, rs1574415799, rs1574462520, rs1085307197, rs1574464060, rs749485755, rs1574464121, rs1574464150, rs1574464160, rs1085307214, rs1574485996, rs1574486497, rs1574486566, rs1574488314, rs1574488346, rs1574488353, rs1574488357, rs1574488412, rs1414031345, rs1574488484, rs1574488490, rs863223419, rs1574489046, rs1574494632, rs1574494655, rs1574500018, rs1574505253, rs1574505321, rs371174955, rs1574506729, rs1574506732, rs1574506781, rs1574506790, rs1574506799, rs1574506914, rs1574506976, rs1574507076, rs1574507124, rs1574507215, rs1574507268, rs1574507272, rs1574507276, rs1574507290, rs1574507331, rs398123042, rs374644720, rs1588573831, rs1592222308, rs1592223392, rs756315327, rs1603248167, rs1397811125, rs1603255267, rs1603255327, rs1603255336, rs1603255339, rs754897911, rs1603256095, rs1085307155, rs1085307156, rs1574464226, rs1085307226, rs1574486038, rs1553508321, rs1574488277, rs1574488501, rs1574493841, rs1574499954

Unknown
Disease term	Disease name	Evidence	References	Source
Otitis media	Otitis Media			ClinVar
Metabolic Syndrome	Metabolic Syndrome			GWAS
Hypertension	Hypertension			GWAS
Diabetes	Diabetes			GWAS

Associations from Text Mining
Disease Name	Relationship Type	References
Atrial Fibrillation	Associate	33594863
Carcinoma Squamous Cell	Associate	34116656
Esophageal Neoplasms	Associate	26631031
Fibrosis	Associate	33594863
Heart Diseases	Associate	33594863
Heart Valve Diseases	Associate	33594863
Inflammation	Associate	31356157
Neoplasm Metastasis	Associate	34511489
Neoplasms	Associate	26631031, 30487700, 34116656
Osteopetrosis	Associate	28592808, 30885997, 39875016
Osteopetrosis mild autosomal recessive form	Associate	23280965, 28592808, 28816234, 29034896, 36526684
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	39453390
Prostatic Neoplasms	Associate	33672425
Stomach Neoplasms	Associate	30487700
Tuberculosis Pulmonary	Associate	35720382
Uterine Cervical Neoplasms	Associate	34116656