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NM_004343.3(CALR):c.1092_1143del52 (p.Leu367Thrfs) AND Thrombocythemia 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 19, 2013
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000083257.5

Allele description [Variation Report for NM_004343.3(CALR):c.1092_1143del52 (p.Leu367Thrfs)]

NM_004343.3(CALR):c.1092_1143del52 (p.Leu367Thrfs)

Gene:
CALR:calreticulin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_004343.3(CALR):c.1092_1143del52 (p.Leu367Thrfs)
HGVS:
  • NC_000019.10:g.12943758_12943809del
  • NG_029662.1:g.10159_10210del
  • NM_004343.4:c.1099_1150delMANE SELECT
  • NP_004334.1:p.Leu367fs
  • LRG_828:g.10159_10210del
  • NC_000019.9:g.13054572_13054623del
  • NM_004343.3:c.1092_1143del52
Note:
52-nt deletion from exon 9 of CALR.
Protein change:
L367fs
Links:
dbVar: nssv3761626; dbVar: nsv1067850; OMIM: 109091.0001; dbSNP: rs1555760738
NCBI 1000 Genomes Browser:
rs1555760738
Molecular consequence:
  • NM_004343.4:c.1099_1150del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Thrombocythemia 1 (THCYT1)
Synonyms:
Idiopathic thrombocythemia; THROMBOCYTOSIS 1; THROMBOCYTHEMIA, SOMATIC
Identifiers:
MONDO: MONDO:0008554; MedGen: C3277671; OMIM: 187950

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000115336OMIM
no assertion criteria provided
Pathogenic
(Dec 19, 2013)
somaticliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedsomaticnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Somatic mutations of calreticulin in myeloproliferative neoplasms.

Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, Them NC, Berg T, Gisslinger B, Pietra D, Chen D, Vladimer GI, Bagienski K, Milanesi C, Casetti IC, Sant'Antonio E, Ferretti V, Elena C, Schischlik F, Cleary C, Six M, Schalling M, et al.

N Engl J Med. 2013 Dec 19;369(25):2379-90. doi: 10.1056/NEJMoa1311347. Epub 2013 Dec 10.

PubMed [citation]
PMID:
24325356

Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2.

Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, Avezov E, Li J, Kollmann K, Kent DG, Aziz A, Godfrey AL, Hinton J, Martincorena I, Van Loo P, Jones AV, Guglielmelli P, Tarpey P, Harding HP, Fitzpatrick JD, Goudie CT, Ortmann CA, et al.

N Engl J Med. 2013 Dec 19;369(25):2391-2405. doi: 10.1056/NEJMoa1312542. Epub 2013 Dec 10.

PubMed [citation]
PMID:
24325359
PMCID:
PMC3966280

Details of each submission

From OMIM, SCV000115336.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Klampfl et al. (2013) and Nangalia et al. (2013) identified a somatic 52-bp deletion in exon 9 of the CALR gene (1092_1143del) in patients with myeloproliferative neoplasms, including myelofibrosis (254450) and essential thrombocythemia (see 187950). CALR mutations and JAK2 and MPL mutations were mutually exclusive. The 52-bp mutation resulted in frameshift and premature termination (L367fsTer46). Klampfl et al. (2013) identified a total of 36 types of somatic insertion or deletion within exon 9 of CALR, all of which caused a frameshift to the same alternative reading frame and generated a novel C-terminal peptide in the mutant calreticulin. Klampfl et al. (2013) identified insertions or deletions in exon 9 of CALR in 88% of individuals with primary myelofibrosis with nonmutated JAK2 or MPL. The 52-bp deletion accounted for 53% of all cases of mutated CALR among several types of myeloproliferative neoplasm. Overexpression of this mutation resulted in cytokine-independent growth in vitro through the activation of STAT5 (601511). Nangalia et al. (2013) identified 23 patients with myelofibrosis who carried the L367fsTer46 mutation. Overall, Nangalia et al. (2013) identified 19 different somatic CALR mutations, all in exon 9 and all of which generated a +1 frameshift resulting in a mutant protein with a novel C terminal. CALR mutations were present in 18 of 32 patients (56%) with primary myelofibrosis and in 12 of 14 patients (86%) with progression of essential thrombocythemia to myelofibrosis. Neither Klampfl et al. (2013) nor Nangalia et al. (2013) detected CALR mutation in individuals with polycythemia vera.

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

Last Updated: Jun 23, 2024