NM_003384.3(VRK1):c.29G>A (p.Gly10Glu) AND Pontocerebellar hypoplasia type 1A

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 12, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002541696.2

Allele description [Variation Report for NM_003384.3(VRK1):c.29G>A (p.Gly10Glu)]

NM_003384.3(VRK1):c.29G>A (p.Gly10Glu)

Gene:

VRK1:VRK serine/threonine kinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q32.2

Genomic location:

Preferred name:

NM_003384.3(VRK1):c.29G>A (p.Gly10Glu)

HGVS:

NC_000014.9:g.96833500G>A
NG_016293.1:g.41154G>A
NM_003384.3:c.29G>AMANE SELECT
NP_003375.1:p.Gly10Glu
NC_000014.8:g.97299837G>A
NM_003384.2:c.29G>A

Protein change:

G10E

Links:

dbSNP: rs777028935

NCBI 1000 Genomes Browser:

rs777028935

Molecular consequence:

NM_003384.3:c.29G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Pontocerebellar hypoplasia type 1A (PCH1A)
Synonyms:: Pontocerebellar hypoplasia with infantile spinal muscular atrophy; Pontocerebellar hypoplasia with anterior horn cell disease
Identifiers:: Gene: 100852400; MONDO: MONDO:0011866; MedGen: C1843504; Orphanet: 2254; Orphanet: 88616; OMIM: 607596

Recent activity

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sn-1-specific diacylglycerol lipase ABHD11 isoform 1 [Mus musculus]
sn-1-specific diacylglycerol lipase ABHD11 isoform 1 [Mus musculus]
gi|21644577|ref|NP_660250.1|

Protein
cytochrome c oxidase subunit 1, partial (mitochondrion) [Phytophthora gibbosa]
cytochrome c oxidase subunit 1, partial (mitochondrion) [Phytophthora gibbosa]
gi|1382811015|gb|AWC68373.1|

Protein
heat shock protein 90, partial [Phytophthora gibbosa]
heat shock protein 90, partial [Phytophthora gibbosa]
gi|310770302|gb|ADP21647.1|

Protein
Cladosporium cladosporioides internal transcribed spacer 1, partial sequence; 5....
Cladosporium cladosporioides internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|2833698465|gb|PQ471462.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003269945	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003269945

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 12, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003269945.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 10 of the VRK1 protein (p.Gly10Glu). This variant is present in population databases (rs777028935, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with VRK1-related conditions. ClinVar contains an entry for this variant (Variation ID: 990857). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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