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NM_003384.3(VRK1):c.464T>A (p.Leu155Ter) AND Inborn genetic diseases

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 12, 2023
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:
RCV003282068.2

Allele description [Variation Report for NM_003384.3(VRK1):c.464T>A (p.Leu155Ter)]

NM_003384.3(VRK1):c.464T>A (p.Leu155Ter)

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.464T>A (p.Leu155Ter)
HGVS:
  • NC_000014.9:g.96852920T>A
  • NG_016293.1:g.60574T>A
  • NM_001411051.1:c.464T>A
  • NM_001411053.1:c.464T>A
  • NM_003384.3:c.464T>AMANE SELECT
  • NP_001397980.1:p.Leu155Ter
  • NP_001397982.1:p.Leu155Ter
  • NP_003375.1:p.Leu155Ter
  • NC_000014.8:g.97319257T>A
  • NM_003384.2:c.464T>A
Protein change:
L155*
Molecular consequence:
  • NM_001411051.1:c.464T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001411053.1:c.464T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_003384.3:c.464T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003975064Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Pathogenic
(May 12, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV003975064.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.464T>A (p.L155*) alteration, located in exon 6 (coding exon 5) of the VRK1 gene, consists of a T to A substitution at nucleotide position 464. This changes the amino acid from a leucine (L) to a stop codon at amino acid position 155. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This allele was reported in one heterozygous individual in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the available evidence, this alteration is classified as pathogenic.

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

Last Updated: May 1, 2024