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Intellectual disability

Gene: VPS51

Amber List (moderate evidence)
VPS51 (VPS51, GARP complex subunit)
EnsemblGeneIds (GRCh38): ENSG00000149823
EnsemblGeneIds (GRCh37): ENSG00000149823
OMIM: 615738, Gene2Phenotype
VPS51 is in 3 panels

3 reviews

Ida Ertmanska (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There are now 4 unrelated patients reported with biallelic VPS51 variants and severe syndromic ID / GDD. Hence, this gene can be promoted to Green at the next update.
Created: 14 May 2026, 1:03 p.m. | Last Modified: 14 May 2026, 1:43 p.m.
Panel Version: 10.14
Additional cases:
PMID: 40565173 Aygun et al., 2025
2 sibs exhibiting developmental delay, a thin corpus callosum, severe intellectual disability, epilepsy, microcephaly, hearing loss, and dysphagia. Both homozygous for a c.1511C>T; p.Thr504Met VPS51 variant.

PMID: 40176246 Bhanudeep & Koneti, 2025
Proband: 15 month old boy with severe global developmental delay, failure to thrive, microcephaly, generalized hypotonia, nystagmus, Brisk DTRs. Neuroimaging showed diffuse hypomyelinated white matter, severely hypoplastic corpus callosum, and cerebral and cerebellar atrophy. WES revealed a homozygous VPS51 duplication p.Lys126_Met132dup.
Created: 14 May 2026, 12:52 p.m. | Last Modified: 14 May 2026, 2:33 p.m.
Panel Version: 10.14

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Pontocerebellar hypoplasia, type 13, OMIM:618606; pontocerebellar hypoplasia, type 13, MONDO:0032831; neurodevelopmental disorder, MONDO:0700092

Publications

Created: 14 May 2026, 12:52 p.m.
Last Modified: 14 May 2026, 2:33 p.m.
Panel version: 10.11

Arina Puzriakova (Genomics England Curator)

I don't know

Comment on list classification: Additional cases are required before inclusion of VPS51 on a diagnostic panel; however, gene added to watchlist.
Created: 31 Jul 2020, 1:05 p.m. | Last Modified: 31 Jul 2020, 1:05 p.m.
Panel Version: 3.213
Associated with phenotype in OMIM,but not in G2P.

PMID: 30624672 (2019) - 6-year-old girl with severe global developmental delay, pontocerebellar abnormalities, microcephaly, hypotonia, epilepsy and several systemic and peripheral dysfunctions. Exome sequencing revealed compound heterozygous variants in VPS51 ([c.2232delC; p.Asp745Thrfs*93];[c.1468C>T; p.Arg490Cys]). Functional studies of both variants indicate impaired function of the mutant protein.

PMID: 31207318 (2019) - two sisters with a homozygous three bp in-frame deletion (c.1419_1421del; p.Phe474del) in VPS51 associated with developmental delay, absent speech, severe ID and microcephaly. Development in both sisters was initially unremarkable; however, following an episode of fever (at 1 and 12 months of age, respectively), pyschomotor development was severely delayed. At 30 months and 9 years of age, respectively, neither sister had any language. No functional studies of the variant or patient cells were undertaken.
Created: 31 Jul 2020, 1:03 p.m. | Last Modified: 31 Jul 2020, 1:03 p.m.
Panel Version: 3.212

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Pontocerebellar hypoplasia, type 13, 618606

Publications

Created: 31 Jul 2020, 1:03 p.m.
Last Modified: 31 Jul 2020, 1:03 p.m.
Panel version: 3.212

Zornitza Stark (Australian Genomics)

I don't know

Two families reported with bi-allelic variants in this gene and global developmental delay, impaired intellectual development with absent speech, microcephaly, and progressive atrophy of the cerebellar vermis and brainstem. Additional features, including seizures and visual impairment, are variable.
Sources: Literature
Created: 2 May 2020, 2:39 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Pontocerebellar hypoplasia, type 13, MIM# 618606

Publications

Created: 2 May 2020, 2:39 a.m.

Panel version: 3.33

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Pontocerebellar hypoplasia, type 13, OMIM:618606
  • pontocerebellar hypoplasia, type 13, MONDO:0032831
  • neurodevelopmental disorder, MONDO:0700092
Tags
Q2_26_promote_green
OMIM
615738
Clinvar variants
Variants in VPS51
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 May 2026, Gel status: 2

Set Phenotypes

Ida Ertmanska (Genomics England Curator)

Phenotypes for gene: VPS51 were changed from Pontocerebellar hypoplasia, type 13, MIM# 618606 to Pontocerebellar hypoplasia, type 13, OMIM:618606; pontocerebellar hypoplasia, type 13, MONDO:0032831; neurodevelopmental disorder, MONDO:0700092

14 May 2026, Gel status: 2

Set publications

Ida Ertmanska (Genomics England Curator)

Publications for gene: VPS51 were set to 30624672; 31207318

14 May 2026, Gel status: 2

Added Tag

Ida Ertmanska (Genomics England Curator)

Tag Q2_26_promote_green tag was added to gene: VPS51.

14 May 2026, Gel status: 2

Entity classified by Genomics England curator

Ida Ertmanska (Genomics England Curator)

Gene: vps51 has been classified as Amber List (Moderate Evidence).

31 Jul 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: vps51 has been classified as Amber List (Moderate Evidence).

2 May 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Zornitza Stark (Australian Genomics)

gene: VPS51 was added gene: VPS51 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: VPS51 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: VPS51 were set to 30624672; 31207318 Phenotypes for gene: VPS51 were set to Pontocerebellar hypoplasia, type 13, MIM# 618606 Review for gene: VPS51 was set to AMBER