VPS36

vacuolar protein sorting 36 homolog, the group of ESCRT-II

Basic information

Region (hg38): 13:52412602-52450634

Previous symbols: [ "C13orf9" ]

Links

ENSG00000136100 ∙ NCBI:51028 ∙ OMIM:610903 ∙ HGNC:20312 ∙ Uniprot:Q86VN1 ∙ 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 VPS36 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS36 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in VPS36

This is a list of pathogenic ClinVar variants found in the VPS36 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52415877-C-G		not specified	Uncertain significance (Feb 26, 2024)
13-52418004-T-G		not specified	Uncertain significance (Dec 27, 2022)
13-52423614-G-A		not specified	Uncertain significance (Aug 30, 2021)
13-52433687-T-C		not specified	Uncertain significance (May 06, 2024)
13-52434872-C-T		not specified	Uncertain significance (Feb 27, 2023)
13-52434873-G-A		not specified	Uncertain significance (Jun 16, 2024)
13-52436301-C-A		not specified	Uncertain significance (Jun 11, 2021)
13-52436342-C-A		not specified	Uncertain significance (Apr 17, 2024)
13-52436399-T-C		not specified	Uncertain significance (Dec 22, 2023)
13-52439149-A-G		not specified	Likely benign (Nov 22, 2021)
13-52442399-A-G		not specified	Uncertain significance (Jan 08, 2024)
13-52442407-G-C		not specified	Uncertain significance (Jun 24, 2022)
13-52450513-C-T		not specified	Uncertain significance (Aug 15, 2023)
13-52450590-T-C		not specified	Uncertain significance (Apr 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS36	protein_coding	protein_coding	ENST00000378060	14	38027

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0464	0.954	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.71	138	207	0.665	0.0000104	2515
Missense in Polyphen		44	73.004	0.60271		857
Synonymous	1.18	59	71.7	0.823	0.00000367	709
Loss of Function	3.59	8	28.7	0.278	0.00000155	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000534	0.000528
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00130	0.00129
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ESCRT-II complex (endosomal sorting complex required for transport II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. Its ability to bind ubiquitin probably plays a role in endosomal sorting of ubiquitinated cargo proteins by ESCRT complexes. The ESCRT-II complex may also play a role in transcription regulation, possibly via its interaction with ELL. Binds phosphoinosides such as PtdIns(3,4,5)P3.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Endosomal Sorting Complex Required For Transport (ESCRT) (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.382
• rvis_EVS: -0.3
• rvis_percentile_EVS: 32.62

Haploinsufficiency Scores

• pHI: 0.0970
• hipred: Y
• hipred_score: 0.704
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vps36

Gene ontology

• Biological process: endosomal transport;macroautophagy;multivesicular body assembly;protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
• Cellular component: ESCRT II complex;nucleus;lysosome;endosome;cytosol;late endosome membrane;extracellular exosome
• Molecular function: protein binding;protein C-terminus binding;phosphatidylinositol-3-phosphate binding;ubiquitin binding