VPS29

VPS29 retromer complex component, the group of Retriever complex

Basic information

Region (hg38): 12:110491083-110502111

Links

ENSG00000111237

∙ NCBI:51699 ∙ OMIM:606932 ∙ HGNC:14340 ∙ Uniprot:Q9UBQ0 ∙ 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 VPS29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS29 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			5 clinvar			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in VPS29

This is a list of pathogenic ClinVar variants found in the VPS29 region.

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

Position	Phenotype	Significance	ClinVar
12-110492109-A-T	not specified	Uncertain significance (Mar 03, 2022)	2228888
12-110493089-G-A	not specified	Uncertain significance (May 14, 2024)	3332232
12-110493230-T-C	not specified	Uncertain significance (Oct 12, 2021)	2226151
12-110496050-C-T	not specified	Uncertain significance (Jan 30, 2024)	3188893
12-110496085-C-G	not specified	Uncertain significance (Mar 20, 2024)	2359517
12-110496110-G-T	not specified	Uncertain significance (Jan 30, 2024)	3188892

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS29	protein_coding	protein_coding	ENST00000360579	5	11021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.747	0.251	124732	0	2	124734	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	49	95.9	0.511	0.00000460	1219
Missense in Polyphen		6	24.001	0.24999		350
Synonymous	0.445	33	36.4	0.906	0.00000178	351
Loss of Function	2.45	1	8.88	0.113	4.59e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000902	0.00000883
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as component of the retromer cargo-selective complex (CSC). The CSC is believed to be the core functional component of retromer or respective retromer complex variants acting to prevent missorting of selected transmembrane cargo proteins into the lysosomal degradation pathway. The recruitment of the CSC to the endosomal membrane involves RAB7A and SNX3. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX3-retromer mediates the retrograde endosome-to-TGN transport of WLS distinct from the SNX-BAR retromer pathway. The SNX27-retromer is believed to be involved in endosome-to-plasma membrane trafficking and recycling of a broad spectrum of cargo proteins. The CSC seems to act as recruitment hub for other proteins, such as the WASH complex and TBC1D5. Required to regulate transcytosis of the polymeric immunoglobulin receptor (pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasma membrane trafficking; the function is dependent of association with ANKRD27 (PubMed:24856514). {ECO:0000250|UniProtKB:Q9QZ88, ECO:0000269|PubMed:16737443, ECO:0000269|PubMed:24856514, ECO:0000303|PubMed:15247922, ECO:0000303|PubMed:21725319, ECO:0000303|PubMed:23563491}.;
Pathway: Endocytosis - Homo sapiens (human);Signaling by WNT;Signal Transduction;serine biosynthesis (phosphorylated route);serine and glycine biosynthesis;WNT ligand biogenesis and trafficking (Consensus)

Recessive Scores

pRec: 0.103

Intolerance Scores

loftool: 0.242
rvis_EVS: 0.08
rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

pHI: 0.454
hipred: Y
hipred_score: 0.531
ghis: 0.649

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vps29
Phenotype

Gene ontology

Biological process: intracellular protein transport;regulation of autophagy;viral process;Wnt signaling pathway;retrograde transport, endosome to Golgi;retrograde transport, endosome to plasma membrane
Cellular component: endosome;early endosome;late endosome;cytosol;endosome membrane;retromer complex;retromer, cargo-selective complex;intracellular membrane-bounded organelle
Molecular function: protein binding;protein transporter activity;metal ion binding