NM_001099403.2(PRDM8):c.1055C>A (p.Pro352Gln) AND Early-onset Lafora body disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 5, 2020
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:: RCV002046435.6

Allele description [Variation Report for NM_001099403.2(PRDM8):c.1055C>A (p.Pro352Gln)]

NM_001099403.2(PRDM8):c.1055C>A (p.Pro352Gln)

Gene:

PRDM8:PR/SET domain 8 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q21.21

Genomic location:

Preferred name:

NM_001099403.2(PRDM8):c.1055C>A (p.Pro352Gln)

HGVS:

NC_000004.12:g.80202517C>A
NG_046725.1:g.22248C>A
NM_001099403.2:c.1055C>AMANE SELECT
NM_020226.4:c.1055C>A
NP_001092873.1:p.Pro352Gln
NP_064611.3:p.Pro352Gln
NC_000004.11:g.81123671C>A

Protein change:

P352Q

Links:

dbSNP: rs1332727339

NCBI 1000 Genomes Browser:

rs1332727339

Molecular consequence:

NM_001099403.2:c.1055C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020226.4:c.1055C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Early-onset Lafora body disease
Synonyms:: Epilepsy, progressive myoclonic, 10
Identifiers:: MONDO: MONDO:0014717; MedGen: C4225258; Orphanet: 324290; OMIM: 616640

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002315339	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 5, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002315339

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 5, 2020)

germline

clinical testing

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

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

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, SCV002315339.3

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

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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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"). This variant has not been reported in the literature in individuals with PRDM8-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces proline with glutamine at codon 352 of the PRDM8 protein (p.Pro352Gln). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and glutamine.

#	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: Sep 29, 2024

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