NM_003384.3(VRK1):c.45A>G (p.Ala15=) AND Pontocerebellar hypoplasia type 1A

Germline classification:: Benign (4 submissions)
Last evaluated:: Feb 1, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000605697.18

Allele description [Variation Report for NM_003384.3(VRK1):c.45A>G (p.Ala15=)]

NM_003384.3(VRK1):c.45A>G (p.Ala15=)

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.45A>G (p.Ala15=)

HGVS:

NC_000014.9:g.96833516A>G
NG_016293.1:g.41170A>G
NM_003384.3:c.45A>GMANE SELECT
NP_003375.1:p.Ala15=
NC_000014.8:g.97299853A>G
NM_003384.2:c.45A>G

Links:

dbSNP: rs2145635

NCBI 1000 Genomes Browser:

rs2145635

Molecular consequence:

NM_003384.3:c.45A>G - synonymous variant - [Sequence Ontology: SO:0001819]

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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Model organism or animal sample from Xiphorhynchus elegans elegans x Xiphorhynch...
Model organism or animal sample from Xiphorhynchus elegans elegans x Xiphorhynchus spixii

biosample
ubiquitin-like domain-containing CTD phosphatase 1 isoform X1 [Mus musculus]
ubiquitin-like domain-containing CTD phosphatase 1 isoform X1 [Mus musculus]
gi|568976460|ref|XP_006534585.1|

Protein
Mus musculus SEC31 homolog A, COPII coat complex component (Sec31a), transcript ...
Mus musculus SEC31 homolog A, COPII coat complex component (Sec31a), transcript variant 7, mRNA
gi|2183243335|ref|NM_001359350.2|

Nucleotide
protein transport protein Sec31A isoform a [Mus musculus]
protein transport protein Sec31A isoform a [Mus musculus]
gi|1318663272|ref|NP_001346252.1|

Protein
SAMN08503719 (1)
SRA

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000389780	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 13, 2018)	germline	clinical testing	Citation Link,
SCV000733415	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Benign	germline	clinical testing
SCV001730717	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002093675	Natera, Inc.	no assertion criteria provided	Benign (Nov 19, 2019)	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 Illumina Laboratory Services, Illumina, SCV000389780.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV000733415.1

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

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001730717.4

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

#	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

From Natera, Inc., SCV002093675.1

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

#	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: Nov 3, 2024

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