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NC_000014.8:g.(?_97319190)_(97325994_?)del AND Pontocerebellar hypoplasia type 1A

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 14, 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:
RCV004578099.2

Allele description [Variation Report for NC_000014.8:g.(?_97319190)_(97325994_?)del]

NC_000014.8:g.(?_97319190)_(97325994_?)del

Gene:
VRK1:VRK serine/threonine kinase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
14q32.2
Genomic location:
Chr14: 97319190 - 97325994 (on Assembly GRCh37)
Preferred name:
NC_000014.8:g.(?_97319190)_(97325994_?)del
HGVS:
NC_000014.8:g.(?_97319190)_(97325994_?)del

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005065567Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Apr 14, 2022) 		unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Spinal muscular atrophy with pontocerebellar hypoplasia is caused by a mutation in the VRK1 gene.

Renbaum P, Kellerman E, Jaron R, Geiger D, Segel R, Lee M, King MC, Levy-Lahad E.

Am J Hum Genet. 2009 Aug;85(2):281-9. doi: 10.1016/j.ajhg.2009.07.006. Epub 2009 Jul 30.

PubMed [citation]
PMID:
19646678
PMCID:
PMC2725266
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005065567.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This variant results in the deletion of exons 7-10 and part of exon 6 (c.397_890-900del) of the VRK1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in VRK1 are known to be pathogenic (PMID: 19646678, 24126608, 27281532). 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: 842535). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024