VPS26B

VPS26 retromer complex component B

Basic information

Region (hg38): 11:134224670-134247788

Links

ENSG00000151502

∙ NCBI:112936 ∙ OMIM:610027 ∙ HGNC:28119 ∙ Uniprot:Q4G0F5 ∙ 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 VPS26B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS26B 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 VPS26B

This is a list of pathogenic ClinVar variants found in the VPS26B region.

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

Position	Phenotype	Significance	ClinVar
11-134225276-C-G	not specified	Uncertain significance (Jul 14, 2021)	2237305
11-134234930-T-C	not specified	Uncertain significance (Aug 26, 2022)	2308878
11-134234953-G-T	not specified	Uncertain significance (Mar 30, 2022)	2280994
11-134243217-C-T	not specified	Uncertain significance (May 17, 2023)	2547706
11-134245469-A-G	not specified	Uncertain significance (Oct 20, 2021)	2255995

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS26B	protein_coding	protein_coding	ENST00000281187	6	23148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.967	0.0335	125654	0	3	125657	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	134	218	0.615	0.0000135	2227
Missense in Polyphen		43	94.597	0.45456		952
Synonymous	-1.40	104	87.4	1.19	0.00000539	633
Loss of Function	3.34	1	14.9	0.0669	8.01e-7	175

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)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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 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. May be involved in retrograde transport of SORT1 but not of IGF2R. Acts redundantly with VSP26A in SNX-27 mediated endocytic recycling of SLC2A1/GLUT1 (By similarity). {ECO:0000250|UniProtKB:O75436, ECO:0000250|UniProtKB:Q8C0E2}.;
Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.117

Intolerance Scores

loftool: 0.0967
rvis_EVS: -0.52
rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

pHI: 0.140
hipred: Y
hipred_score: 0.749
ghis: 0.624

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Vps26b
Phenotype

Gene ontology

Biological process: intracellular protein transport;regulation of macroautophagy;retrograde transport, endosome to Golgi;cellular response to interferon-gamma
Cellular component: endosome;early endosome;late endosome;cytosol;retromer complex;retromer, cargo-selective complex;phagocytic vesicle
Molecular function: protein binding;protein transporter activity