NM_016553.5(NUP62):c.731C>A (p.Thr244Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 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:: RCV003019055.10

Allele description [Variation Report for NM_016553.5(NUP62):c.731C>A (p.Thr244Asn)]

NM_016553.5(NUP62):c.731C>A (p.Thr244Asn)

Genes:

IL4I1:interleukin 4 induced 1 [Gene - OMIM - HGNC]
NUP62:nucleoporin 62 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.33

Genomic location:

Preferred name:

NM_016553.5(NUP62):c.731C>A (p.Thr244Asn)

HGVS:

NC_000019.10:g.49909077G>T
NG_021170.1:g.25429C>A
NG_023448.1:g.25655C>A
NM_001193357.2:c.731C>A
NM_001258017.2:c.-227-4756C>A
NM_001258018.2:c.-285-4756C>A
NM_012346.5:c.731C>A
NM_016553.5:c.731C>AMANE SELECT
NM_153718.4:c.731C>A
NM_153719.4:c.731C>A
NM_172374.3:c.-227-4756C>A
NP_001180286.1:p.Thr244Asn
NP_036478.2:p.Thr244Asn
NP_057637.2:p.Thr244Asn
NP_714940.1:p.Thr244Asn
NP_714941.1:p.Thr244Asn
NC_000019.9:g.50412334G>T

Protein change:

T244N

Molecular consequence:

NM_001258017.2:c.-227-4756C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001258018.2:c.-285-4756C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_172374.3:c.-227-4756C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001193357.2:c.731C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_012346.5:c.731C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_016553.5:c.731C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_153718.4:c.731C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_153719.4:c.731C>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
SCV003311556	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 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

SCV003311556

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 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, SCV003311556.2

#	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 threonine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 244 of the NUP62 protein (p.Thr244Asn). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with NUP62-related conditions. ClinVar contains an entry for this variant (Variation ID: 2097929). 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 disruptive. 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.

#	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 3, 2024

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Relating variation to medicine