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NM_152906.7(TANGO2):c.4del (p.Cys2fs) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Nov 6, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001589106.5

Allele description [Variation Report for NM_152906.7(TANGO2):c.4del (p.Cys2fs)]

NM_152906.7(TANGO2):c.4del (p.Cys2fs)

Gene:
TANGO2:transport and golgi organization 2 homolog [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
22q11.21
Genomic location:
Preferred name:
NM_152906.7(TANGO2):c.4del (p.Cys2fs)
HGVS:
  • NC_000022.11:g.20036802del
  • NG_046857.1:g.24803del
  • NM_001283106.3:c.4del
  • NM_001283116.3:c.4del
  • NM_001283129.3:c.-114del
  • NM_001283148.3:c.4del
  • NM_001283154.3:c.4del
  • NM_001283179.3:c.4del
  • NM_001283186.3:c.4del
  • NM_001283199.3:c.4del
  • NM_001283215.3:c.-114del
  • NM_001283235.3:c.-176del
  • NM_001283248.3:c.4del
  • NM_001322141.2:c.-114del
  • NM_001322142.2:c.4del
  • NM_001322143.2:c.-114del
  • NM_001322144.2:c.-114del
  • NM_001322145.2:c.-114del
  • NM_001322146.2:c.-176del
  • NM_001322147.2:c.-114del
  • NM_001322148.2:c.-416del
  • NM_001322149.2:c.-114del
  • NM_001322150.2:c.-416del
  • NM_001322153.2:c.-176del
  • NM_001322155.2:c.-176del
  • NM_001322160.2:c.-176del
  • NM_001322163.2:c.4del
  • NM_001322166.2:c.4del
  • NM_001322167.2:c.4del
  • NM_001322169.2:c.4del
  • NM_001322171.2:c.-176del
  • NM_001322172.2:c.-416del
  • NM_001322173.2:c.-416del
  • NM_001322174.2:c.-176del
  • NM_001322175.2:c.-176del
  • NM_152906.7:c.4delMANE SELECT
  • NP_001270035.1:p.Cys2fs
  • NP_001270045.1:p.Cys2fs
  • NP_001270077.1:p.Cys2fs
  • NP_001270083.1:p.Cys2fs
  • NP_001270108.1:p.Cys2fs
  • NP_001270115.1:p.Cys2fs
  • NP_001270128.1:p.Cys2fs
  • NP_001270177.1:p.Cys2fs
  • NP_001309071.1:p.Cys2fs
  • NP_001309092.1:p.Cys2fs
  • NP_001309095.1:p.Cys2fs
  • NP_001309096.1:p.Cys2fs
  • NP_001309098.1:p.Cys2fs
  • NP_690870.3:p.Cys2fs
  • NC_000022.10:g.20024325del
  • NM_152906.4:c.4del
  • NM_152906.5:c.4delT
  • NR_104274.3:n.68del
  • NR_104275.3:n.68del
  • NR_136206.2:n.180del
  • NR_136211.2:n.180del
  • NR_136212.1:n.182del
Protein change:
C2fs
Links:
OMIM: 616830.0005; dbSNP: rs869320693
NCBI 1000 Genomes Browser:
rs869320693
Molecular consequence:
  • NM_001283129.3:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001283215.3:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001283235.3:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322141.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322143.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322144.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322145.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322146.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322147.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322148.2:c.-416del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322149.2:c.-114del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322150.2:c.-416del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322153.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322155.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322160.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322171.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322172.2:c.-416del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322173.2:c.-416del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322174.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001322175.2:c.-176del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001283106.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283116.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283148.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283154.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283179.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283186.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283199.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001283248.3:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322142.2:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322163.2:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322166.2:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322167.2:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001322169.2:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_152906.7:c.4del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_104274.3:n.68del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_104275.3:n.68del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136206.2:n.180del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136211.2:n.180del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136212.1:n.182del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001824901GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(May 27, 2020) 		germlineclinical testing

Citation Link,

SCV003444529Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 6, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 GeneDx, SCV001824901.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 26805782)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV003444529.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Cys2Alafs*35) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of TANGO2-related conditions (PMID: 26805782). ClinVar contains an entry for this variant (Variation ID: 224773). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 5, 2024