VPS50

Chr 7q21.2-q21.3

VPS50 subunit of EARP/GARPII complex

Aliases:: KIAA1861, FLJ20097, DKFZp313I2429, VPS54L
MANE:: ENST00000305866.10

OMIM: 616465 ↗NCBI: 55610 ↗Ensembl ↗

Annotations refreshed 11 hours ago.

Predicted protein structure

AlphaFold predicted structure

VPS50 · Q96JG6

v62025-08-01

Predicted Aligned Error matrix for VPS50 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

70.7/ 100

Confident

964 residues

Confidence breakdown

Very high(≥ 90)10%
Confident(70–90)54%
Low(50–70)19%
Very low(< 50)17%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Fetal anomalies
BIALLELIC, autosomal or pseudoautosomal
Cholestasis
BIALLELIC, autosomal or pseudoautosomal
Early onset or syndromic epilepsy
BIALLELIC, autosomal or pseudoautosomal
Intellectual disability
BIALLELIC, autosomal or pseudoautosomal
Malformations of cortical development
BIALLELIC, autosomal or pseudoautosomal
Severe microcephaly
BIALLELIC, autosomal or pseudoautosomal
Monogenic short stature
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

neurodevelopmental disorder with microcephaly, seizures, and neonatal cholestasis
0.59
nutritional deficiency disease
0.26
placenta praevia
0.25
macular degeneration
0.24
glomerulonephritis
0.24
arthropathy
0.24
gastric cancer
0.07
Abnormality of the skeletal system
0.07
liver disorder
0.04
corneal dystrophy
0.03

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Syndetin

Acts as a component of the EARP complex that is involved in endocytic recycling. The EARP complex associates with Rab4-positive endosomes and promotes recycling of internalized transferrin receptor (TFRC) to the plasma membrane. Within the EARP complex, required to tether the complex to recycling endosomes. Not involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN)