VPS28

VPS28 subunit of ESCRT-I, the group of ESCRT-I

Basic information

Region (hg38): 8:144423600-144428563

Links

ENSG00000160948 ∙ NCBI:51160 ∙ OMIM:611952 ∙ HGNC:18178 ∙ Uniprot:Q9UK41 ∙ 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 VPS28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS28 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			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	2	0

Variants in VPS28

This is a list of pathogenic ClinVar variants found in the VPS28 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-144423896-G-A		not specified	Likely benign (Feb 06, 2024)
8-144423927-G-A		not specified	Uncertain significance (Mar 13, 2023)
8-144423973-C-T		not specified	Uncertain significance (Mar 27, 2023)
8-144424053-G-A		not specified	Uncertain significance (Dec 27, 2023)
8-144424072-C-T		not specified	Uncertain significance (Jan 23, 2024)
8-144424084-G-A		not specified	Uncertain significance (Dec 15, 2023)
8-144424221-C-A		not specified	Uncertain significance (Aug 28, 2021)
8-144424246-T-C		not specified	Uncertain significance (Apr 12, 2023)
8-144424745-G-A		not specified	Likely benign (Oct 30, 2023)
8-144424789-T-C		not specified	Uncertain significance (Mar 20, 2024)
8-144424809-G-A		not specified	Uncertain significance (Jun 11, 2024)
8-144425731-A-G		not specified	Uncertain significance (Jun 07, 2024)
8-144426038-C-T		not specified	Uncertain significance (Feb 27, 2023)
8-144426193-G-A		not specified	Uncertain significance (Apr 26, 2023)
8-144426199-T-C		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS28	protein_coding	protein_coding	ENST00000377348	8	4932

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0693	0.919	125552	0	9	125561	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.871	127	158	0.805	0.0000104	1508
Missense in Polyphen		20	42.377	0.47196		421
Synonymous	-1.21	75	62.8	1.19	0.00000429	452
Loss of Function	2.19	4	12.3	0.326	7.02e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000587	0.0000587
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000563	0.0000544
Finnish	0.000187	0.000185
European (Non-Finnish)	0.0000198	0.0000176
Middle Eastern	0.0000563	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular trafficking process. {ECO:0000269|PubMed:11916981}.
• Pathway: Endocytosis - Homo sapiens (human);Disease;Vesicle-mediated transport;Membrane Trafficking;Assembly Of The HIV Virion;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease;Membrane binding and targetting of GAG proteins;Synthesis And Processing Of GAG, GAGPOL Polyproteins (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.215
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.201
• hipred: Y
• hipred_score: 0.723
• ghis: 0.607

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vps28

Gene ontology

• Biological process: endosomal transport;macroautophagy;viral life cycle;negative regulation of protein ubiquitination;multivesicular body assembly;viral budding via host ESCRT complex;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;positive regulation of protein catabolic process;positive regulation of ubiquitin-dependent endocytosis
• Cellular component: ESCRT I complex;cytoplasm;endosome;early endosome;cytosol;plasma membrane;endosome membrane;late endosome membrane;extracellular exosome
• Molecular function: protein binding;ubiquitin binding;protein-containing complex binding