NM_152906.7(TANGO2):c.491G>A (p.Trp164Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 17, 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:: RCV003686410.2

Allele description [Variation Report for NM_152906.7(TANGO2):c.491G>A (p.Trp164Ter)]

NM_152906.7(TANGO2):c.491G>A (p.Trp164Ter)

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.491G>A (p.Trp164Ter)

HGVS:

NC_000022.11:g.20061569G>A
NG_046857.1:g.49570G>A
NM_001283106.3:c.491G>A
NM_001283116.3:c.491G>A
NM_001283129.3:c.614G>A
NM_001283148.3:c.491G>A
NM_001283154.3:c.491G>A
NM_001283179.3:c.305G>A
NM_001283186.3:c.305G>A
NM_001283199.3:c.381-1769G>A
NM_001283215.3:c.575-2973G>A
NM_001283235.3:c.197G>A
NM_001283248.3:c.266-1769G>A
NM_001322141.2:c.614G>A
NM_001322142.2:c.491G>A
NM_001322143.2:c.614G>A
NM_001322144.2:c.614G>A
NM_001322145.2:c.428G>A
NM_001322146.2:c.389G>A
NM_001322147.2:c.428G>A
NM_001322148.2:c.389G>A
NM_001322149.2:c.504-1769G>A
NM_001322150.2:c.197G>A
NM_001322153.2:c.197G>A
NM_001322155.2:c.197G>A
NM_001322160.2:c.389G>A
NM_001322163.2:c.305G>A
NM_001322166.2:c.305G>A
NM_001322167.2:c.305G>A
NM_001322169.2:c.305G>A
NM_001322171.2:c.197G>A
NM_001322172.2:c.197G>A
NM_001322173.2:c.197G>A
NM_001322174.2:c.197G>A
NM_001322175.2:c.197G>A
NM_152906.7:c.491G>AMANE SELECT
NP_001270035.1:p.Trp164Ter
NP_001270045.1:p.Trp164Ter
NP_001270058.1:p.Trp205Ter
NP_001270077.1:p.Trp164Ter
NP_001270083.1:p.Trp164Ter
NP_001270108.1:p.Trp102Ter
NP_001270115.1:p.Trp102Ter
NP_001270164.1:p.Trp66Ter
NP_001309070.1:p.Trp205Ter
NP_001309071.1:p.Trp164Ter
NP_001309072.1:p.Trp205Ter
NP_001309073.1:p.Trp205Ter
NP_001309074.1:p.Trp143Ter
NP_001309075.1:p.Trp130Ter
NP_001309076.1:p.Trp143Ter
NP_001309077.1:p.Trp130Ter
NP_001309079.1:p.Trp66Ter
NP_001309082.1:p.Trp66Ter
NP_001309084.1:p.Trp66Ter
NP_001309089.1:p.Trp130Ter
NP_001309092.1:p.Trp102Ter
NP_001309095.1:p.Trp102Ter
NP_001309096.1:p.Trp102Ter
NP_001309098.1:p.Trp102Ter
NP_001309100.1:p.Trp66Ter
NP_001309101.1:p.Trp66Ter
NP_001309102.1:p.Trp66Ter
NP_001309103.1:p.Trp66Ter
NP_001309104.1:p.Trp66Ter
NP_690870.3:p.Trp164Ter
NC_000022.10:g.20049092G>A
NR_136206.2:n.481G>A
NR_136211.2:n.667G>A
NR_136212.1:n.588G>A

Protein change:

W102*

Molecular consequence:

NM_001283199.3:c.381-1769G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001283215.3:c.575-2973G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001283248.3:c.266-1769G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001322149.2:c.504-1769G>A - intron variant - [Sequence Ontology: SO:0001627]
NR_136206.2:n.481G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136211.2:n.667G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136212.1:n.588G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001283106.3:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283116.3:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283129.3:c.614G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283148.3:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283154.3:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283179.3:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283186.3:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001283235.3:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322141.2:c.614G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322142.2:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322143.2:c.614G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322144.2:c.614G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322145.2:c.428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322146.2:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322147.2:c.428G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322148.2:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322150.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322153.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322155.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322160.2:c.389G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322163.2:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322166.2:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322167.2:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322169.2:c.305G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322171.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322172.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322173.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322174.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001322175.2:c.197G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_152906.7:c.491G>A - nonsense - [Sequence Ontology: SO:0001587]

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
SCV004423479	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26805781, 26805782, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004423479

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 17, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Recurrent Muscle Weakness with Rhabdomyolysis, Metabolic Crises, and Cardiac Arrhythmia Due to Bi-allelic TANGO2 Mutations.

Lalani SR, Liu P, Rosenfeld JA, Watkin LB, Chiang T, Leduc MS, Zhu W, Ding Y, Pan S, Vetrini F, Miyake CY, Shinawi M, Gambin T, Eldomery MK, Akdemir ZH, Emrick L, Wilnai Y, Schelley S, Koenig MK, Memon N, Farach LS, Coe BP, et al.

Am J Hum Genet. 2016 Feb 4;98(2):347-57. doi: 10.1016/j.ajhg.2015.12.008. Epub 2016 Jan 21.

PubMed [citation]

PMID:: 26805781
PMCID:: PMC4746334

Bi-allelic Truncating Mutations in TANGO2 Cause Infancy-Onset Recurrent Metabolic Crises with Encephalocardiomyopathy.

Kremer LS, Distelmaier F, Alhaddad B, Hempel M, Iuso A, Küpper C, Mühlhausen C, Kovacs-Nagy R, Satanovskij R, Graf E, Berutti R, Eckstein G, Durbin R, Sauer S, Hoffmann GF, Strom TM, Santer R, Meitinger T, Klopstock T, Prokisch H, Haack TB.

Am J Hum Genet. 2016 Feb 4;98(2):358-62. doi: 10.1016/j.ajhg.2015.12.009. Epub 2016 Jan 21.

PubMed [citation]

PMID:: 26805782
PMCID:: PMC4746337

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004423479.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TANGO2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Trp164*) in the TANGO2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TANGO2 are known to be pathogenic (PMID: 26805781, 26805782).

#	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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