NM_001100913.3(PACS2):c.58G>A (p.Val20Met) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 24, 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:: RCV003770827.2

Allele description [Variation Report for NM_001100913.3(PACS2):c.58G>A (p.Val20Met)]

NM_001100913.3(PACS2):c.58G>A (p.Val20Met)

Genes:

LOC130056677:ATAC-STARR-seq lymphoblastoid silent region 6228 [Gene]
BRF1:BRF1 general transcription factor IIIB subunit [Gene - OMIM - HGNC]
PACS2:phosphofurin acidic cluster sorting protein 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q32.33

Genomic location:

Preferred name:

NM_001100913.3(PACS2):c.58G>A (p.Val20Met)

HGVS:

NC_000014.9:g.105314976G>A
NG_029489.1:g.5602C>T
NG_191098.1:g.107G>A
NM_001100913.3:c.58G>AMANE SELECT
NM_001242786.2:c.-162+346C>T
NM_001242787.2:c.-162+346C>T
NM_001243127.3:c.-83+13997G>A
NM_015197.4:c.58G>A
NP_001094383.2:p.Val20Met
NP_056012.2:p.Val20Met
NC_000014.8:g.105781313G>A
NM_001100913.2:c.58G>A

Protein change:

V20M

Links:

dbSNP: rs2058502984

NCBI 1000 Genomes Browser:

rs2058502984

Molecular consequence:

NM_001242786.2:c.-162+346C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001242787.2:c.-162+346C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001243127.3:c.-83+13997G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001100913.3:c.58G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015197.4:c.58G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV004618177	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 24, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 32725632, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004618177

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 24, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Whole-exome sequencing in adult patients with developmental and epileptic encephalopathy: It is never too late.

Minardi R, Licchetta L, Baroni MC, Pippucci T, Stipa C, Mostacci B, Severi G, Toni F, Bergonzini L, Carelli V, Seri M, Tinuper P, Bisulli F.

Clin Genet. 2020 Nov;98(5):477-485. doi: 10.1111/cge.13823. Epub 2020 Sep 1.

PubMed [citation]

PMID:: 32725632

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004618177.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1029076). This missense change has been observed in individual(s) with clinical features of PACS2-related conditions (PMID: 32725632; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 20 of the PACS2 protein (p.Val20Met).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 24, 2024

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