SNX17

sorting nexin 17, the group of Sorting nexins

Basic information

Region (hg38): 2:27370496-27377535

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.

not_specified (47 variants)
SNX17-related_disorder (3 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. These statistics are base on transcript: NM_000014748.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	3	0

Loading clinvar variants...

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