NM_152906.7(TANGO2):c.52T>A (p.Tyr18Asn) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 24, 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:: RCV002828757.3

Allele description [Variation Report for NM_152906.7(TANGO2):c.52T>A (p.Tyr18Asn)]

NM_152906.7(TANGO2):c.52T>A (p.Tyr18Asn)

Gene:

TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q11.21

Genomic location:

Preferred name:

NM_152906.7(TANGO2):c.52T>A (p.Tyr18Asn)

HGVS:

NC_000022.11:g.20036850T>A
NG_046857.1:g.24851T>A
NM_001283106.3:c.52T>A
NM_001283116.3:c.52T>A
NM_001283129.3:c.-66T>A
NM_001283148.3:c.52T>A
NM_001283154.3:c.52T>A
NM_001283179.3:c.52T>A
NM_001283186.3:c.52T>A
NM_001283199.3:c.52T>A
NM_001283215.3:c.-66T>A
NM_001283235.3:c.-128T>A
NM_001283248.3:c.52T>A
NM_001322141.2:c.-66T>A
NM_001322142.2:c.52T>A
NM_001322143.2:c.-66T>A
NM_001322144.2:c.-66T>A
NM_001322145.2:c.-66T>A
NM_001322146.2:c.-128T>A
NM_001322147.2:c.-66T>A
NM_001322148.2:c.-368T>A
NM_001322149.2:c.-66T>A
NM_001322150.2:c.-368T>A
NM_001322153.2:c.-128T>A
NM_001322155.2:c.-128T>A
NM_001322160.2:c.-128T>A
NM_001322163.2:c.52T>A
NM_001322166.2:c.52T>A
NM_001322167.2:c.52T>A
NM_001322169.2:c.52T>A
NM_001322171.2:c.-128T>A
NM_001322172.2:c.-368T>A
NM_001322173.2:c.-368T>A
NM_001322174.2:c.-128T>A
NM_001322175.2:c.-128T>A
NM_152906.7:c.52T>AMANE SELECT
NP_001270035.1:p.Tyr18Asn
NP_001270045.1:p.Tyr18Asn
NP_001270077.1:p.Tyr18Asn
NP_001270083.1:p.Tyr18Asn
NP_001270108.1:p.Tyr18Asn
NP_001270115.1:p.Tyr18Asn
NP_001270128.1:p.Tyr18Asn
NP_001270177.1:p.Tyr18Asn
NP_001309071.1:p.Tyr18Asn
NP_001309092.1:p.Tyr18Asn
NP_001309095.1:p.Tyr18Asn
NP_001309096.1:p.Tyr18Asn
NP_001309098.1:p.Tyr18Asn
NP_690870.3:p.Tyr18Asn
NC_000022.10:g.20024373T>A
NR_104274.3:n.116T>A
NR_104275.3:n.116T>A
NR_136206.2:n.228T>A
NR_136211.2:n.228T>A
NR_136212.1:n.230T>A

Protein change:

Y18N

Molecular consequence:

NM_001283129.3:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001283215.3:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001283235.3:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322141.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322143.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322144.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322145.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322146.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322147.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322148.2:c.-368T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322149.2:c.-66T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322150.2:c.-368T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322153.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322155.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322160.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322171.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322172.2:c.-368T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322173.2:c.-368T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322174.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322175.2:c.-128T>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001283106.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283116.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283148.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283154.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283179.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283186.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283199.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001283248.3:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322142.2:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322163.2:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322166.2:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322167.2:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001322169.2:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152906.7:c.52T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_104274.3:n.116T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_104275.3:n.116T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136206.2:n.228T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136211.2:n.228T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136212.1:n.230T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV003213773	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 24, 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

SCV003213773

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 24, 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, SCV003213773.2

#	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 not present in population databases (gnomAD no frequency). This sequence change replaces tyrosine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 18 of the TANGO2 protein (p.Tyr18Asn). This variant has not been reported in the literature in individuals affected with TANGO2-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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available").

#	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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