NM_018052.5(VAC14):c.2005G>T (p.Val669Leu) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 6, 2024
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:: RCV001662820.3

Allele description [Variation Report for NM_018052.5(VAC14):c.2005G>T (p.Val669Leu)]

NM_018052.5(VAC14):c.2005G>T (p.Val669Leu)

Gene:

VAC14:VAC14 component of PIKFYVE complex [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_018052.5(VAC14):c.2005G>T (p.Val669Leu)

HGVS:

NC_000016.10:g.70695574C>A
NG_054902.1:g.110596G>T
NM_001351157.2:c.1303G>T
NM_018052.5:c.2005G>TMANE SELECT
NP_001338086.1:p.Val435Leu
NP_060522.3:p.Val669Leu
NC_000016.9:g.70729477C>A
NM_018052.3:c.2005G>T

Protein change:

V435L

Links:

dbSNP: rs1363536856

NCBI 1000 Genomes Browser:

rs1363536856

Molecular consequence:

NM_001351157.2:c.1303G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_018052.5:c.2005G>T - missense variant - [Sequence Ontology: SO:0001583]

Functional consequence:

variation affecting protein [Variation Ontology: 0002]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001872884	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Nov 6, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001872884

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Nov 6, 2024)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV001872884.2

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27292112, 31876398, 32949958, 31387860)

#	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

Last Updated: Nov 18, 2024

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