NM_001099403.2(PRDM8):c.929G>T (p.Gly310Val) AND Early-onset Lafora body disease

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 11, 2022
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:: RCV003069925.3

Allele description [Variation Report for NM_001099403.2(PRDM8):c.929G>T (p.Gly310Val)]

NM_001099403.2(PRDM8):c.929G>T (p.Gly310Val)

Genes:

LOC129992744:ATAC-STARR-seq lymphoblastoid silent region 15521 [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.929G>T (p.Gly310Val)

HGVS:

NC_000004.12:g.80202391G>T
NG_046725.1:g.22122G>T
NM_001099403.2:c.929G>TMANE SELECT
NM_020226.4:c.929G>T
NP_001092873.1:p.Gly310Val
NP_064611.3:p.Gly310Val
NC_000004.11:g.81123545G>T

Protein change:

G310V

Molecular consequence:

NM_001099403.2:c.929G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_020226.4:c.929G>T - 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

Recent activity

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Homo sapiens THAP domain containing 8 (THAP8), mRNA
Homo sapiens THAP domain containing 8 (THAP8), mRNA
gi|22749336|ref|NM_152658.1|

Nucleotide
ATP synthase beta chain, partial (chloroplast) [Athyrium sp. Ebihara A 110849]
ATP synthase beta chain, partial (chloroplast) [Athyrium sp. Ebihara A 110849]
gi|1304380602|gb|AUD08353.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003470734	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 11, 2022)	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

SCV003470734

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 11, 2022)

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, SCV003470734.2

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 310 of the PRDM8 protein (p.Gly310Val). 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with PRDM8-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database.

#	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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