SNX33

sorting nexin 33, the group of PX-BAR domain containing

Basic information

Region (hg38): 15:75647912-75662301

Previous symbols: [ "SH3PX3" ]

Links

ENSG00000173548 ∙ NCBI:257364 ∙ OMIM:619107 ∙ HGNC:28468 ∙ Uniprot:Q8WV41 ∙ 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 SNX33 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNX33 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			39	1		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in SNX33

This is a list of pathogenic ClinVar variants found in the SNX33 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75649119-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-75649135-T-C			Likely benign (Apr 01, 2023)
15-75649277-G-A		not specified	Likely benign (Jan 20, 2023)
15-75649280-C-T		not specified	Uncertain significance (Feb 25, 2025)
15-75649331-T-A		not specified	Uncertain significance (Jun 10, 2024)
15-75649332-C-T		not specified	Uncertain significance (Jun 10, 2024)
15-75649341-C-T		not specified	Uncertain significance (Oct 06, 2021)
15-75649376-A-C		not specified	Uncertain significance (May 28, 2024)
15-75649401-G-A		not specified	Uncertain significance (Feb 23, 2023)
15-75649409-C-G		not specified	Uncertain significance (Nov 09, 2024)
15-75649421-G-C		not specified	Uncertain significance (Mar 07, 2023)
15-75649438-T-G		not specified	Uncertain significance (Dec 15, 2022)
15-75649446-A-G		not specified	Uncertain significance (Nov 22, 2022)
15-75649484-G-A		not specified	Uncertain significance (Oct 26, 2022)
15-75649493-C-T		not specified	Uncertain significance (Jan 17, 2024)
15-75649502-G-A		not specified	Uncertain significance (Sep 29, 2022)
15-75649548-G-C		not specified	Uncertain significance (Jan 26, 2022)
15-75649551-C-T		not specified	Uncertain significance (Jan 21, 2025)
15-75649577-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-75649581-C-T		not specified	Uncertain significance (Mar 14, 2023)
15-75649598-C-T		not specified	Uncertain significance (Mar 07, 2025)
15-75649602-A-G		not specified	Uncertain significance (Feb 17, 2024)
15-75649637-G-A		not specified	Uncertain significance (Jun 26, 2024)
15-75649726-C-G		not specified	Uncertain significance (Jun 13, 2022)
15-75649727-G-A		not specified	Uncertain significance (Jan 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SNX33	protein_coding	protein_coding	ENST00000308527	2	14396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0841	0.914	125719	0	14	125733	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.79	259	354	0.733	0.0000226	3829
Missense in Polyphen		107	190.43	0.56188		2037
Synonymous	1.47	114	136	0.839	0.00000809	1102
Loss of Function	2.73	5	17.2	0.290	9.05e-7	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000722	0.0000703
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the reorganization of the cytoskeleton, endocytosis and cellular vesicle trafficking via its interactions with membranes, WASL, DNM1 and DNM2. Acts both during interphase and at the end of mitotic cell divisions. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Modulates endocytosis of cell-surface proteins, such as APP and PRNP; this then modulates the secretion of APP and PRNP peptides. Promotes membrane tubulation (in vitro). May promote the formation of macropinosomes. {ECO:0000269|PubMed:18353773, ECO:0000269|PubMed:18419754, ECO:0000269|PubMed:19487689, ECO:0000269|PubMed:20964629, ECO:0000269|PubMed:21048941, ECO:0000269|PubMed:22718350}.
• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.471
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.150
• hipred: Y
• hipred_score: 0.736
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.349

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Snx33

Gene ontology

• Biological process: mitotic cytokinesis;intracellular protein transport;endocytosis;endosome organization;endosomal transport;protein import;cleavage furrow formation;macropinocytosis;negative regulation of endocytosis;positive regulation of membrane protein ectodomain proteolysis;plasma membrane tubulation;negative regulation of protein localization to cell surface;positive regulation of protein localization to cell surface
• Cellular component: cytosol;membrane;extrinsic component of membrane;cytoplasmic vesicle membrane;cytoplasmic vesicle
• Molecular function: protein binding;phosphatidylinositol binding;identical protein binding