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NM_018052.5(VAC14):c.1987G>A (p.Ala663Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 25, 2021
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:
RCV001981490.4

Allele description [Variation Report for NM_018052.5(VAC14):c.1987G>A (p.Ala663Thr)]

NM_018052.5(VAC14):c.1987G>A (p.Ala663Thr)

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.1987G>A (p.Ala663Thr)
HGVS:
  • NC_000016.10:g.70695592C>T
  • NG_054902.1:g.110578G>A
  • NM_001351157.2:c.1285G>A
  • NM_018052.5:c.1987G>AMANE SELECT
  • NP_001338086.1:p.Ala429Thr
  • NP_060522.3:p.Ala663Thr
  • NC_000016.9:g.70729495C>T
Protein change:
A429T
Links:
dbSNP: rs190751684
NCBI 1000 Genomes Browser:
rs190751684
Molecular consequence:
  • NM_001351157.2:c.1285G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_018052.5:c.1987G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002222366Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 25, 2021) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Invitae, SCV002222366.2

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

Description

This sequence change replaces alanine with threonine at codon 663 of the VAC14 protein (p.Ala663Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. This variant is present in population databases (rs190751684, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with VAC14-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Dec 24, 2023