NM_006277.3(ITSN2):c.2153G>A (p.Arg718Gln) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 18, 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:: RCV002756065.3

Allele description [Variation Report for NM_006277.3(ITSN2):c.2153G>A (p.Arg718Gln)]

NM_006277.3(ITSN2):c.2153G>A (p.Arg718Gln)

Gene:

ITSN2:intersectin 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p23.3

Genomic location:

Preferred name:

NM_006277.3(ITSN2):c.2153G>A (p.Arg718Gln)

HGVS:

NC_000002.12:g.24271870C>T
NG_029516.1:g.93659G>A
NM_001348181.2:c.2111G>A
NM_001348182.2:c.2072G>A
NM_001348183.2:c.2072G>A
NM_001348184.2:c.2030G>A
NM_001348185.2:c.2153G>A
NM_001348186.2:c.2072G>A
NM_006277.2:c.2153G>A
NM_006277.3:c.2153G>AMANE SELECT
NM_019595.4:c.2072G>A
NM_147152.3:c.2153G>A
NP_001335110.1:p.Arg704Gln
NP_001335111.1:p.Arg691Gln
NP_001335112.1:p.Arg691Gln
NP_001335113.1:p.Arg677Gln
NP_001335114.1:p.Arg718Gln
NP_001335115.1:p.Arg691Gln
NP_006268.2:p.Arg718Gln
NP_062541.3:p.Arg691Gln
NP_671494.2:p.Arg718Gln
NC_000002.11:g.24494739C>T

Protein change:

R677Q

Molecular consequence:

NM_001348181.2:c.2111G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348182.2:c.2072G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348183.2:c.2072G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348184.2:c.2030G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348185.2:c.2153G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348186.2:c.2072G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006277.3:c.2153G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_019595.4:c.2072G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_147152.3:c.2153G>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
SCV003026074	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 18, 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

SCV003026074

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 18, 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, SCV003026074.2

#	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 missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with ITSN2-related conditions. This variant is present in population databases (rs551809311, gnomAD 0.08%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 718 of the ITSN2 protein (p.Arg718Gln).

#	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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