NM_152383.5(DIS3L2):c.1253C>A (p.Pro418Gln) AND Perlman syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 22, 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:: RCV003844593.2

Allele description [Variation Report for NM_152383.5(DIS3L2):c.1253C>A (p.Pro418Gln)]

NM_152383.5(DIS3L2):c.1253C>A (p.Pro418Gln)

Gene:

DIS3L2:DIS3 like 3'-5' exoribonuclease 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q37.1

Genomic location:

Preferred name:

NM_152383.5(DIS3L2):c.1253C>A (p.Pro418Gln)

HGVS:

NC_000002.12:g.232238581C>A
NG_032572.1:g.281999C>A
NM_001257281.2:c.1253C>A
NM_152383.5:c.1253C>AMANE SELECT
NP_001244210.1:p.Pro418Gln
NP_689596.4:p.Pro418Gln
NP_689596.4:p.Pro418Gln
LRG_534t1:c.1253C>A
LRG_534:g.281999C>A
LRG_534p1:p.Pro418Gln
NC_000002.11:g.233103291C>A
NM_152383.4:c.1253C>A
NR_046476.2:n.1399C>A
NR_046477.2:n.1375C>A

Protein change:

P418Q

Molecular consequence:

NM_001257281.2:c.1253C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152383.5:c.1253C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046476.2:n.1399C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_046477.2:n.1375C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Perlman syndrome (PRLMNS)
Synonyms:: Renal hamartomas nephroblastomatosis and fetal gigantism; Nephroblastomatosis fetal ascites macrosomia and wilms tumor
Identifiers:: MONDO: MONDO:0009965; MedGen: C0796113; Orphanet: 2849; OMIM: 267000

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Apoc2 apolipoprotein C2 [Rattus norvegicus]
Apoc2 apolipoprotein C2 [Rattus norvegicus]
Gene ID:292697

Gene
Abcc2 ATP binding cassette subfamily C member 2 [Rattus norvegicus]
Abcc2 ATP binding cassette subfamily C member 2 [Rattus norvegicus]
Gene ID:25303

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004648851	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 22, 2023)	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

SCV004648851

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 22, 2023)

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, SCV004648851.1

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

Description

This variant is present in population databases (rs752820747, gnomAD 0.0009%). This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 418 of the DIS3L2 protein (p.Pro418Gln). This variant has not been reported in the literature in individuals affected with DIS3L2-related conditions. 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt DIS3L2 protein function.

#	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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