SNX17

sorting nexin 17, the group of Sorting nexins

Basic information

Region (hg38): 2:27370495-27377535

Links

ENSG00000115234 ∙ NCBI:9784 ∙ OMIM:605963 ∙ HGNC:14979 ∙ Uniprot:Q15036 ∙ 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 SNX17 gene.

• Inborn genetic diseases (13 variants)
• Retinitis pigmentosa (12 variants)
• Retinitis Pigmentosa, Dominant (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX17 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			12	1		13
Total	0	0	25	1	0

Variants in SNX17

This is a list of pathogenic ClinVar variants found in the SNX17 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27370796-C-T		not specified	Uncertain significance (Nov 09, 2023)
2-27372648-T-C		not specified	Uncertain significance (Nov 27, 2023)
2-27372665-C-G		not specified	Uncertain significance (Mar 31, 2023)
2-27373308-A-G		SNX17-related disorder	Likely benign (Mar 02, 2021)
2-27373897-G-A		not specified	Uncertain significance (Feb 22, 2023)
2-27373979-G-A			Likely benign (Jul 01, 2022)
2-27374152-A-G		not specified	Uncertain significance (Oct 06, 2023)
2-27374351-C-T		not specified	Uncertain significance (Mar 23, 2022)
2-27374352-G-A		not specified	Uncertain significance (Aug 17, 2022)
2-27374385-C-G		not specified	Uncertain significance (Jun 24, 2022)
2-27374721-T-C		not specified	Uncertain significance (Sep 30, 2021)
2-27375525-C-T		not specified	Uncertain significance (May 08, 2023)
2-27375548-C-T		not specified	Uncertain significance (Jul 26, 2022)
2-27375604-C-T		SNX17-related disorder	Likely benign (Mar 30, 2022)
2-27375606-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-27375680-C-T		not specified	Uncertain significance (Jun 21, 2021)
2-27375681-G-A		not specified	Uncertain significance (Sep 29, 2023)
2-27375892-G-A		not specified	Uncertain significance (Nov 18, 2022)
2-27376169-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-27376326-G-A		not specified	Uncertain significance (Feb 28, 2024)
2-27376338-C-T		not specified	Uncertain significance (Aug 21, 2023)
2-27376353-A-C		SNX17-related disorder	Likely benign (Apr 12, 2022)
2-27376367-G-A		not specified	Uncertain significance (May 17, 2023)
2-27376385-C-T		not specified	Uncertain significance (Dec 26, 2023)
2-27376609-A-C		not specified	Uncertain significance (Dec 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX17	protein_coding	protein_coding	ENST00000233575	15	6607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00220	0.998	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.778	250	287	0.871	0.0000180	3043
Missense in Polyphen		44	77.135	0.57043		940
Synonymous	-1.55	128	108	1.19	0.00000587	941
Loss of Function	3.30	10	29.3	0.341	0.00000149	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Critical regulator of endosomal recycling of numerous receptors, channels, and other transmembrane proteins. Binds to NPxY sequences in the cytoplasmic tails of target cargos. Plays a role in the sorting of endocytosed LRP1 and APP, and prevents their degradation. Required for maintenance of normal cell surface levels of APP and LRP1. Recycles internalized integrins ITGB1, ITGB5 and their associated alpha subunits, preventing them from lysosomal degradation. Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)). {ECO:0000269|PubMed:15121882, ECO:0000269|PubMed:15769472, ECO:0000269|PubMed:16712798, ECO:0000269|PubMed:19005208, ECO:0000269|PubMed:21512128, ECO:0000269|PubMed:22492727}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.460
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.442
• hipred: N
• hipred_score: 0.402
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx17
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: cardiac septum development;cholesterol catabolic process;intracellular protein transport;receptor-mediated endocytosis;signal transduction;endosomal transport;regulation of endocytosis;aorta development;coronary vasculature development;retrograde transport, endosome to plasma membrane
• Cellular component: endosome;early endosome;Golgi apparatus;cytosol;endosome membrane;membrane;cytoplasmic vesicle membrane;cytoplasmic vesicle;protein-containing complex;intracellular membrane-bounded organelle
• Molecular function: signaling receptor binding;protein binding;protein C-terminus binding;phosphatidylinositol binding;low-density lipoprotein particle receptor binding