VCV000989335.4 - ClinVar

NM_014264.5(PLK4):c.126+1G>A

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_014264.5(PLK4):c.126+1G>A

Variation ID: 989335 Accession: VCV000989335.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 4q28.1 4: 127881927 (GRCh38) [ NCBI UCSC ] 4: 128803082 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 23, 2020	Dec 23, 2020	Aug 7, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NM_014264.5:c.126+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001190799.2:c.126+1G>A		splice donor
NM_001190801.2:c.3+1G>A		splice donor
NC_000004.12:g.127881927G>A
NC_000004.11:g.128803082G>A
NG_041821.1:g.6067G>A

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000004.12:127881926:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

dbSNP: rs1456235557 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PLK4		-	-	GRCh38 GRCh37	579	624

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
PLK4-related microcephaly and growth failure with or without ocular features	Likely pathogenic (1)	criteria provided, single submitter	Aug 7, 2020	RCV001270840.4

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Aug 07, 2020)	criteria provided, single submitter (ICSLVariantClassificationCriteria RUGD 01 April 2020) Method: clinical testing	PLK4-related microcephaly and growth failure with or without ocular features Affected status: unknown Allele origin: unknown	Illumina Laboratory Services, Illumina Accession: SCV001451609.1 First in ClinVar: Dec 23, 2020 Last updated: Dec 23, 2020	Comment: The PLK4 c.126+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt the normal gene product. A literature search was … (more) The PLK4 c.126+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is not found in the Genome Aggregation Database in a region of good sequencing coverage, so the variant is presumed to be rare. Experimental data evaluating the impacts of the c.126+1G>A variant at the transcript and protein level are unavailable. Of note, while this variant has the potential to result in an in-frame event, it is also located within the protein kinase domain and is therefore predicted to be damaging. Based on the collective evidence and application of ACMG criteria, the c.126+1G>A variant is classified as likely pathogenic for PLK4-related microcephaly and growth failure with or without ocular features. (less)

Comment:

The PLK4 c.126+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt the normal gene product. A literature search was performed for the gene and cDNA change. No publications were found based on this search. This variant is not found in the Genome Aggregation Database in a region of good sequencing coverage, so the variant is presumed to be rare. Experimental data evaluating the impacts of the c.126+1G>A variant at the transcript and protein level are unavailable. Of note, while this variant has the potential to result in an in-frame event, it is also located within the protein kinase domain and is therefore predicted to be damaging. Based on the collective evidence and application of ACMG criteria, the c.126+1G>A variant is classified as likely pathogenic for PLK4-related microcephaly and growth failure with or without ocular features.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1456235557 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 10, 2023

ClinVar Genomic variation as it relates to human health

NM_014264.5(PLK4):c.126+1G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1456235557 ...