SNX5

sorting nexin 5, the group of PX-BAR domain containing|Sorting nexins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 20:17941596-17968980

Links

ENSG00000089006 ∙ NCBI:27131 ∙ OMIM:605937 ∙ HGNC:14969 ∙ Uniprot:Q9Y5X3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SNX5 gene.

• Inborn genetic diseases (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX5 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in SNX5

This is a list of pathogenic ClinVar variants found in the SNX5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-17942377-C-G		not specified	Uncertain significance (Oct 20, 2023)
20-17947501-C-T		not specified	Uncertain significance (Dec 17, 2021)
20-17947533-T-C		not specified	Uncertain significance (Dec 01, 2022)
20-17947537-G-T		not specified	Uncertain significance (Feb 13, 2024)
20-17947575-C-T		not specified	Uncertain significance (May 31, 2023)
20-17947588-G-C		not specified	Uncertain significance (Mar 06, 2023)
20-17947590-G-A		not specified	Uncertain significance (Feb 05, 2024)
20-17947608-T-C		not specified	Uncertain significance (Jan 19, 2024)
20-17947630-G-A		not specified	Uncertain significance (Oct 12, 2021)
20-17947642-G-C		not specified	Uncertain significance (Mar 20, 2023)
20-17947645-C-G		not specified	Uncertain significance (Aug 21, 2023)
20-17948892-T-C		not specified	Uncertain significance (Nov 18, 2022)
20-17948906-T-C		not specified	Uncertain significance (Jun 22, 2021)
20-17948925-G-A		not specified	Uncertain significance (Dec 15, 2022)
20-17950344-T-C		not specified	Uncertain significance (Dec 18, 2023)
20-17952621-C-T		not specified	Uncertain significance (Aug 10, 2021)
20-17954093-C-T		not specified	Uncertain significance (Jun 28, 2023)
20-17954107-G-A		not specified	Uncertain significance (Feb 14, 2023)
20-17955378-T-C		not specified	Uncertain significance (Oct 26, 2022)
20-17956960-G-C		not specified	Uncertain significance (May 04, 2022)
20-17957006-T-C		not specified	Uncertain significance (May 10, 2023)
20-17957016-G-C		not specified	Uncertain significance (Sep 01, 2021)
20-17968383-G-C		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX5	protein_coding	protein_coding	ENST00000377768	13	27383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00145	0.997	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.139	204	210	0.973	0.0000108	2690
Missense in Polyphen		58	70.846	0.81868		961
Synonymous	-0.575	84	77.6	1.08	0.00000417	725
Loss of Function	2.81	9	23.8	0.379	0.00000132	298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000514
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000489	0.000489
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3- phosphate (PtdIns(3P)) or phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) (PubMed:15561769). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC) (Probable). Does not have in vitro vesicle-to-membrane remodeling activity (PubMed:23085988). Involved in retrograde transport of lysosomal enzyme receptor IGF2R (PubMed:17148574, PubMed:18596235). May function as link between endosomal transport vesicles and dynactin (Probable). Plays a role in the internalization of EGFR after EGF stimulation (Probable). Involved in EGFR endosomal sorting and degradation; the function involves PIP5K1C isoform 3 and is retromer-independent (PubMed:23602387). Together with PIP5K1C isoform 3 facilitates HGS interaction with ubiquitinated EGFR, which initiates EGFR sorting to intraluminal vesicles (ILVs) of the multivesicular body for subsequent lysosomal degradation (Probable). Involved in E-cadherin sorting and degradation; inhibits PIP5K1C isoform 3-mediated E-cadherin degradation (PubMed:24610942). Plays a role in macropinocytosis (PubMed:18854019, PubMed:21048941). {ECO:0000269|PubMed:18854019, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:24610942, ECO:0000303|PubMed:15561769, ECO:0000303|PubMed:19619496, ECO:0000303|PubMed:23085988}.
• Pathway: Endocytosis - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.208

Intolerance Scores

• loftool: 0.812
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.110
• hipred: Y
• hipred_score: 0.745
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.997

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Snx5
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; respiratory system phenotype; pigmentation phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: snx5
• Affected structure: Muller cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: intracellular protein transport;pinocytosis;epidermal growth factor catabolic process;regulation of macroautophagy;positive regulation of renal sodium excretion;retrograde transport, endosome to Golgi;negative regulation of blood pressure
• Cellular component: ruffle;phagocytic cup;cytosol;brush border;cytoplasmic vesicle membrane;retromer complex;retromer, tubulation complex;extrinsic component of cytoplasmic side of plasma membrane;extrinsic component of endosome membrane;early endosome membrane;macropinocytic cup;tubular endosome
• Molecular function: protein binding;phosphatidylinositol-5-phosphate binding;D1 dopamine receptor binding;dynactin binding;phosphatidylinositol binding;cadherin binding;protein heterodimerization activity;phosphatidylinositol-4-phosphate binding;phosphatidylinositol-3,5-bisphosphate binding