SNX9

sorting nexin 9, the group of PX-BAR domain containing|Sorting nexins

Basic information

Region (hg38): 6:157700387-157945077

Links

ENSG00000130340 ∙ NCBI:51429 ∙ OMIM:605952 ∙ HGNC:14973 ∙ Uniprot:Q9Y5X1 ∙ 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 SNX9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX9 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				1		1
missense			12	1	1	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	12	3	1

Variants in SNX9

This is a list of pathogenic ClinVar variants found in the SNX9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-157867628-A-G		not specified	Uncertain significance (Nov 21, 2022)
6-157896831-G-A		not specified	Uncertain significance (Aug 23, 2021)
6-157896916-G-C		not specified	Likely benign (Dec 19, 2023)
6-157901911-T-C			Likely benign (Jun 28, 2018)
6-157901933-G-T		not specified	Uncertain significance (Apr 25, 2022)
6-157901948-T-A		not specified	Uncertain significance (May 17, 2023)
6-157901963-G-A			Benign (Aug 16, 2018)
6-157902008-C-T		not specified	Uncertain significance (May 13, 2024)
6-157906205-C-T		not specified	Uncertain significance (Apr 22, 2022)
6-157909704-A-C		not specified	Uncertain significance (Jan 11, 2023)
6-157909722-G-A		not specified	Uncertain significance (May 26, 2024)
6-157909955-A-T		not specified	Uncertain significance (Dec 21, 2022)
6-157909983-T-C		not specified	Uncertain significance (Feb 13, 2023)
6-157921522-C-T			Likely benign (Jul 31, 2018)
6-157921645-A-T		not specified	Uncertain significance (Jun 07, 2023)
6-157932267-A-C		not specified	Uncertain significance (Jun 29, 2023)
6-157936048-C-T			Benign (Dec 28, 2017)
6-157938637-C-G		not specified	Uncertain significance (Nov 08, 2021)
6-157940913-T-C		not specified	Uncertain significance (Aug 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX9	protein_coding	protein_coding	ENST00000392185	18	121814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.706	0.294	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	237	330	0.718	0.0000178	3939
Missense in Polyphen		97	161.36	0.60116		1952
Synonymous	1.42	96	115	0.832	0.00000666	1057
Loss of Function	4.62	8	39.2	0.204	0.00000199	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000327	0.0000327
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000462	0.000462
European (Non-Finnish)	0.000151	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in endocytosis and intracellular vesicle trafficking, both during interphase and at the end of mitosis. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Promotes internalization of TNFR. Promotes degradation of EGFR after EGF signaling. Stimulates the GTPase activity of DNM1. Promotes DNM1 oligomerization. Promotes activation of the Arp2/3 complex by WASL, and thereby plays a role in the reorganization of the F- actin cytoskeleton. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Has lower affinity for membranes enriched in phosphatidylinositol 3-phosphate. {ECO:0000269|PubMed:11799118, ECO:0000269|PubMed:12952949, ECO:0000269|PubMed:15703209, ECO:0000269|PubMed:17609109, ECO:0000269|PubMed:17948057, ECO:0000269|PubMed:18388313, ECO:0000269|PubMed:20427313, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}.
• Pathway: EGF-Ncore;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis (Consensus)

Recessive Scores

• pRec: 0.180

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.173
• hipred: Y
• hipred_score: 0.756
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx9

Gene ontology

• Biological process: mitotic cytokinesis;intracellular protein transport;endocytosis;receptor-mediated endocytosis;endosomal transport;positive regulation of protein oligomerization;cleavage furrow formation;positive regulation of GTPase activity;positive regulation of protein kinase activity;positive regulation of membrane protein ectodomain proteolysis;lipid tube assembly;membrane organization;plasma membrane tubulation
• Cellular component: ruffle;cytoplasm;trans-Golgi network;cytosol;plasma membrane;clathrin-coated vesicle;cytoplasmic vesicle membrane;extrinsic component of cytoplasmic side of plasma membrane;cytoplasmic vesicle;extracellular exosome
• Molecular function: protein binding;1-phosphatidylinositol binding;ubiquitin protein ligase binding;phosphatidylinositol binding;identical protein binding;protein homodimerization activity;cadherin binding;Arp2/3 complex binding