NM_152383.5(DIS3L2):c.161T>C (p.Met54Thr) AND Perlman syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 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:: RCV003816261.3

Allele description [Variation Report for NM_152383.5(DIS3L2):c.161T>C (p.Met54Thr)]

NM_152383.5(DIS3L2):c.161T>C (p.Met54Thr)

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.161T>C (p.Met54Thr)

HGVS:

NC_000002.12:g.232015622T>C
NG_032572.1:g.59040T>C
NM_001257281.2:c.161T>C
NM_001257282.2:c.161T>C
NM_152383.5:c.161T>CMANE SELECT
NP_001244210.1:p.Met54Thr
NP_001244211.1:p.Met54Thr
NP_689596.4:p.Met54Thr
NP_689596.4:p.Met54Thr
LRG_534t1:c.161T>C
LRG_534:g.59040T>C
LRG_534p1:p.Met54Thr
NC_000002.11:g.232880332T>C
NM_152383.4:c.161T>C
NR_046476.2:n.307T>C
NR_046477.2:n.307T>C

Protein change:

M54T

Molecular consequence:

NM_001257281.2:c.161T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001257282.2:c.161T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_152383.5:c.161T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_046476.2:n.307T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_046477.2:n.307T>C - 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

Recent activity

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603387430F1 NIH_MGC_87 Homo sapiens cDNA clone IMAGE:5396118 5', mRNA sequence
603387430F1 NIH_MGC_87 Homo sapiens cDNA clone IMAGE:5396118 5', mRNA sequence
gi|16001054|gnl|dbEST|9723529|gb|BI 7.1|

Nucleotide
Drosophila sechellia strain Rob3c scaffold_7772 genomic scaffold, whole genome s...
Drosophila sechellia strain Rob3c scaffold_7772 genomic scaffold, whole genome shotgun sequence
gi|92410963|gb|CH682677.1||gnl|WGS: scaffold_7772

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004614239	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 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

SCV004614239

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 22, 2023)

germline

clinical testing

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

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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, SCV004614239.1

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. This variant has not been reported in the literature in individuals affected with DIS3L2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 54 of the DIS3L2 protein (p.Met54Thr).

#	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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