SNX14 (sorting nexin 14)

Gene

• Entrez ID: 57231
• Gene name: Sorting nexin 14
• Gene symbol: SNX14
• Synonyms (NCBI Gene): RGS-PX2, SCAR20
• Chromosome: 6
• Chromosome location: 6q14.3
• Summary: This gene encodes a member of the sorting nexin family. Members of this family have a phox (PX) phosphoinositide binding domain and are involved in intracellular trafficking. The encoded protein also contains a regulator of G protein signaling (RGS) domai

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200277996	C>T	Likely-pathogenic	Splice donor variant, intron variant
rs201128942	C>A,T	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, intron variant, stop gained, missense variant
rs202176779	T>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs749656742	C>A,G	Likely-pathogenic, pathogenic	Splice donor variant
rs760752847	G>A	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant, non coding transcript variant
rs774694340	A>-	Pathogenic	Non coding transcript variant, stop gained, genic downstream transcript variant, downstream transcript variant, coding sequence variant
rs786205229	G>A	Pathogenic	Non coding transcript variant, stop gained, 5 prime UTR variant, coding sequence variant
rs869320748	->T	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, frameshift variant, non coding transcript variant
rs876657385	G>A,C	Pathogenic	Stop gained, coding sequence variant, missense variant, non coding transcript variant
rs876657386	C>A	Pathogenic	Splice donor variant
rs876657387	A>T	Pathogenic	5 prime UTR variant, stop gained, coding sequence variant, intron variant, non coding transcript variant
rs1057519561	->AAAAAAAAAAA	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1064793681	GTCCAAT>-	Pathogenic	Non coding transcript variant, coding sequence variant, intron variant, genic downstream transcript variant, stop gained
rs1311909367	A>-,AA	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, stop gained, frameshift variant
rs1554226470	->T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1562374476	A>T	Likely-pathogenic	5 prime UTR variant, coding sequence variant, non coding transcript variant, stop gained
rs1582697948	C>A	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1377047	hsa-miR-1324	CLIP-seq
MIRT1377048	hsa-miR-2277-3p	CLIP-seq
MIRT1377049	hsa-miR-3129-3p	CLIP-seq
MIRT1377050	hsa-miR-3942-3p	CLIP-seq
MIRT1377051	hsa-miR-4282	CLIP-seq
MIRT1377052	hsa-miR-513a-3p	CLIP-seq
MIRT1377047	hsa-miR-1324	CLIP-seq
MIRT1377048	hsa-miR-2277-3p	CLIP-seq
MIRT1377050	hsa-miR-3942-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005764	Component	Lysosome	IDA	25848753
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005770	Component	Late endosome	IBA
GO:0005770	Component	Late endosome	IDA	25848753
GO:0005829	Component	Cytosol	IDA
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0030425	Component	Dendrite	IEA
GO:0031902	Component	Late endosome membrane	IEA
GO:0035091	Function	Phosphatidylinositol binding	IBA
GO:0035091	Function	Phosphatidylinositol binding	IEA
GO:0042995	Component	Cell projection	IEA
GO:0045202	Component	Synapse	IEA
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	IDA	25848753
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	IEA
GO:0097352	Process	Autophagosome maturation	IBA
GO:0097352	Process	Autophagosome maturation	IMP	25848753
GO:0098794	Component	Postsynapse	IEA
GO:0099170	Process	Postsynaptic modulation of chemical synaptic transmission	IEA

Other IDs

• MIM: 616105
• HGNC: 14977
• e!Ensembl: ENSG00000135317

Protein

• UniProt ID: Q9Y5W7
• Protein name: Sorting nexin-14
• Protein function: Plays a role in maintaining normal neuronal excitability and synaptic transmission. May be involved in several stages of intracellular trafficking (By similarity). Required for autophagosome clearance, possibly by mediating the fusion of lysosom
• PDB: 4BGJ, 4PQO, 4PQP
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02194	PXA	130 → 299	PXA domain	Family
  PF00615	RGS	336 → 467	Regulator of G protein signaling domain	Domain
  PF00787	PX	603 → 686	PX domain	Domain
  PF08628	Nexin_C	807 → 911	Sorting nexin C terminal	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed both in fetal and adult tissues. {ECO:0000269|PubMed:25848753}.
• Sequence:

  MVPWVRTMGQKLKQRLRLDVGREICRQYPLFCFLLLCLSAASLLLNRYIHILMIFWSFVA
  GVVTFYCSLGPDSLLPNIFFTIKYKPKQLGLQELFPQGHSCAVCGKVKCKRHRPSLLLEN
  YQPWLDLKISSKVDASLSEVLELVLENFVYPWYRDVTDDESFVDELRITLRFFASVLIRR
  IHKVDIPSIITKKLLKAAMKHIEVIVKARQKVKNTEFLQQAALEEYGPELHVALRSRRDE
  LHYLRKLTELLFPYILPPKATDCRSLTLLIREILSGSVFLPSLDFLADPDTVNHLLIIFI
  DDSPPEKATEPASPLVPFLQKFAEPRNKKPSVLKLELKQIREQQDLLFRFMNFLKQEGAV
  HVLQFCLTVEEFNDRILRPELSNDEMLSLHEELQKIYKTYCLDESIDKIRFDPFIVEEIQ
  RIAEGPYIDVVKLQTMRCLFEAYEHVLSLLENVFTPMFCHSDEYFRQLLRGAESPTRNSK
  LNRGSLSLDDFRNTQKRGESFGISRIGSKIKGVFKSTTMEGAMLPNYGVAEGEDDFIEEG
  IVVMEDDSPVEAVSTPNTPRNLAAWKISIPYVDFFEDPSSERKEKKERIPVFCIDVERND
  RRAVGHEPEHWSVYRRYLEFYVLESKLTEFHGAFPDAQLPSKRIIGPKNYEFLKSKREEF
  QEYLQKLLQHPELSNSQLLADFLSPNGGETQFLDKILPDVNLGKIIKSVPGKLMKEKGQH
  LEPFIMNFINSCESPKPKPSRPELTILSPTSENNKKLFNDLFKNNANRAENTERKQNQNY
  FMEVMTVEGVYDYLMYVGRVVFQVPDWLHHLLMGTRILFKNTLEMYTDYYLQCKLEQLFQ
  EHRLVSLITLLRDAIFCENTEPRSLQDKQKGAKQTFEEMMNYIPDLLVKCIGEETKYESI
  RLLFDGLQQPVLNKQLTYVLLDIVIQELFPELNKVQKEVTSVTSWM

• Sequence length: 946

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormal brain morphology	Likely pathogenic	rs1554226470	RCV000454285	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal recessive spinocerebellar ataxia 20	Likely pathogenic; Pathogenic	rs1171657935, rs876657385, rs869320748, rs876657386, rs786205229, rs876657387, rs774694340, rs2537570239, rs951344311, rs201128942, rs2535291703, rs1008167271, rs1329394489, rs1057519561, rs200277996, rs760752847, rs1562374476, rs1311909367, rs749656742, rs1784370895	RCV001783786 RCV000170502 RCV000170504 RCV000170505 RCV000170506 RCV000170507 RCV000170508 RCV003132604 RCV003315269 RCV000498500 RCV003315105 RCV003315114 RCV003315118 RCV001808789 RCV000416984 RCV001824804 RCV000625883 RCV000785947 RCV000984947 RCV000987749 RCV001198150	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cerebellar ataxia	Likely pathogenic	rs1786449736	RCV001775502	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic	rs1786449736	RCV001775502	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Likely pathogenic; Pathogenic	rs769742160	RCV001374927	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SNX14-related disorder	Likely pathogenic; Pathogenic	rs1171657935, rs876657386	RCV003416452 RCV004752768	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar atrophy	Pathogenic	rs786205229	RCV004798794	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic; Pathogenic	rs749656742	RCV005900793 RCV005912149	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATAXIA, SPINOCEREBELLAR	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY, COARSE FACE, MACROCEPHALY, CEREBELLAR HYPOTROPHY SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY-COARSE FACE-MACROCEPHALY-CEREBELLAR HYPOTROPHY SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 20	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIAS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Alzheimer Disease	Associate	26417591	★☆☆☆☆ Found in Text Mining only
Astrocytoma	Associate	36070312	★☆☆☆☆ Found in Text Mining only
Cerebellar Ataxia	Associate	25439728, 29635513	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebellar Diseases	Associate	25439728	★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Associate	32736695	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Associate	25439728	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Associate	25439728	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Megalencephaly	Associate	25439728	★☆☆☆☆ Found in Text Mining only
Seizures	Associate	25439728	★☆☆☆☆ Found in Text Mining only
Spinocerebellar ataxia 20	Associate	27913285, 29635513	★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxias	Associate	27913285	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous Cell Carcinoma of Head and Neck	Associate	31517839	★☆☆☆☆ Found in Text Mining only