1-43337929-T-A
Variant names:
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_005373.3(MPL):c.79+2T>A variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.000191 in 1,609,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00019 ( 0 hom. )
Consequence
MPL
NM_005373.3 splice_donor, intron
NM_005373.3 splice_donor, intron
Scores
4
2
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 4.03
Genes affected
MPL (HGNC:7217): (MPL proto-oncogene, thrombopoietin receptor) In 1990 an oncogene, v-mpl, was identified from the murine myeloproliferative leukemia virus that was capable of immortalizing bone marrow hematopoietic cells from different lineages. In 1992 the human homologue, named, c-mpl, was cloned. Sequence data revealed that c-mpl encoded a protein that was homologous with members of the hematopoietic receptor superfamily. Presence of anti-sense oligodeoxynucleotides of c-mpl inhibited megakaryocyte colony formation. The ligand for c-mpl, thrombopoietin, was cloned in 1994. Thrombopoietin was shown to be the major regulator of megakaryocytopoiesis and platelet formation. The protein encoded by the c-mpl gene, CD110, is a 635 amino acid transmembrane domain, with two extracellular cytokine receptor domains and two intracellular cytokine receptor box motifs . TPO-R deficient mice were severely thrombocytopenic, emphasizing the important role of CD110 and thrombopoietin in megakaryocyte and platelet formation. Upon binding of thrombopoietin CD110 is dimerized and the JAK family of non-receptor tyrosine kinases, as well as the STAT family, the MAPK family, the adaptor protein Shc and the receptors themselves become tyrosine phosphorylated. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PP5
Variant 1-43337929-T-A is Pathogenic according to our data. Variant chr1-43337929-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 135563.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MPL | ENST00000372470.9 | c.79+2T>A | splice_donor_variant, intron_variant | Intron 1 of 11 | 1 | NM_005373.3 | ENSP00000361548.3 | |||
| MPL | ENST00000413998.7 | c.79+2T>A | splice_donor_variant, intron_variant | Intron 1 of 11 | 1 | ENSP00000414004.3 | ||||
| MPL | ENST00000638732.1 | n.79+2T>A | splice_donor_variant, intron_variant | Intron 1 of 9 | 1 |
Frequencies
GnomAD3 genomes 0.000184 AC: 28AN: 152112Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000402 AC: 97AN: 241170Hom.: 0 AF XY: 0.000437 AC XY: 57AN XY: 130414
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:16Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital amegakaryocytic thrombocytopenia Pathogenic:5
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Dec 20, 2019 | NM_005373.2(MPL):c.79+2T>A is classified as pathogenic in the context of congenital amegakaryocytic thrombocytopenia. Sources cited for classification include the following: PMID 21489838 and 16470591. Classification of NM_005373.2(MPL):c.79+2T>A is based on the following criteria: The variant is located at a canonical splice site, is expected to disrupt gene function and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Feb 28, 2017 | The c.79+2T>A variant in MPL has been reported in the homozygous state in 2 indi viduals with congenital amegakaryocyctic thrombocytopenia (CAMT; Germeshausen 20 06, Jalas 2011). It has also been identified in 0.8% (80/9916) of Ashkenazi Jewi sh chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadin stitute.org/; dbSNP rs146249964), and is suggested to be a founder variant in th e Ashkenazi Jewish population (Jalas 2011). This variant occurs in the invariant region (+/- 1,2) of the splice consensus sequence and is predicted to cause alt ered splicing leading to an abnormal or absent protein. Loss of function of the MPL gene is an established mechanism of disease. In summary, although additional studies are required to fully establish its clinical significance, the c.79+2T> A variant is likely pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | - | - - |
| Pathogenic, no assertion criteria provided | curation | Reproductive Health Research and Development, BGI Genomics | Jan 06, 2020 | NG_007525.1(NM_005373.2):c.79+2T>A in the MPL gene has an allele frequency of 0.008 in Ashkenazi Jewish subpopulation in the gnomAD database. This variant is located on a biological transcript and leads to exon skipping or use of a cryptic splice site disrupts reading frame and is therefore predicted to undergo NMD. It has been reported as a founder mutation the Ashkenazi Jewish population (PMID: 21489838). This variant has been reported in homozygous state in two patients with Amegakaryocytic Thrombocytopenia (PMID: 16470591; 21489838). Taken together, we interprete this variant as Pathogenic/Likely pathogenic variant. ACMG/AMP criteria applied: PVS1; PM3; PP4 - |
| Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Oct 24, 2016 | Variant summary: The MPL c.79+2T>A variant involves the alteration of a splice donor site in intron 1, which 5/5 splice prediction tools predict the removal this splice donor site, however, functional studies have yet to be performed to assess these predictions. This variant was found in 58/100444 control chromosomes at a frequency of 0.0005774, which does not exceed the estimated maximal expected allele frequency of a pathogenic MPL variant (0.002357). This variant has been reported in two patients with Amegakaryocytic Thrombocytopenia in homozygous state (Germeshausen_2006 and Jalas_2011). It has also been reported as germline variant in patients with Breast Cancer, Non-Small Cell Lung Cancer, Melanoma and Non-Seminomatous Germ Cell Tumor (Schrader_2016). The variant is a founder mutation in Ashkenazi Jewish population with a carrier frequency of 1 in 75 (Jalas_2011). One clinical diagnostic laboratory in ClinVar classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. - |
not provided Pathogenic:4
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The MPL c.79+2T>A variant was identified in the literature as a homozygous variant in two unrelated patients with congenital amegakaryocytic thrombocytopenia (CAMT) (Germeshausen_2006_PMID:16470591; Jalas_2011_PMID:21489838). In a sample of 2018 individuals of Ashkenazi Jewish descent, the variant was found to have a carrier frequency of 1 in 75 (Jalas_2011_PMID:21489838). The variant was identified in dbSNP (ID: rs146249964) and ClinVar (classified as pathogenic by GeneDx, Integrated Genetics, Counsyl and Fulgent Genetics, and as likely pathogenic by Laboratory for Molecular Medicine, Invitae, Illumina and NIHR Bioresource Rare Diseases, University of Cambridge). The variant was identified in control databases in 97 of 259028 chromosomes at a frequency of 0.0003745 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: Ashkenazi Jewish in 81 of 9646 chromosomes (freq: 0.008397), Other in 4 of 6556 chromosomes (freq: 0.00061) and European (non-Finnish) in 12 of 113480 chromosomes (freq: 0.000106), but was not observed in the African, Latino, East Asian, European (Finnish), or South Asian populations. The c.79+2T>A variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence. In addition, four of four in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a difference in splicing and the loss of the canonical 5' splice site. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 04, 2021 | DNA sequence analysis of the MPL gene demonstrated a sequence change in the canonical splice donor site of intron 1, c.79+2T>A. This sequence change has been described in the gnomAD database with an overall frequency of 0.03% (dbSNP rs146249964) and a frequency of 0.8% in the Ashkenazi Jewish population. The variant is regarded as a founder mutation in the Ashkenazi Jewish population with a carrier frequency of 1 in 75 (PMID: 21489838). This sequence change is predicted to disrupt RNA splicing and likely result in an absent or disrupted protein product. This sequence change has been previously reported in the homozygous state in individuals with congenital amegakaryocytic thrombocytopenia (PMID: 16470591, 21489838). Collectively these evidences suggest that, the c.79+2T>A change is pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 06, 2022 | Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 26822949, 21489838, 31064749, 24728327, 16470591, 27415407, 26556299, 29625052, 31589614) - |
| Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 24, 2022 | - - |
MPL-related disorder Pathogenic:2
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 20, 2024 | The MPL c.79+2T>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in patients with autosomal recessive congenital amegakaryocytic thrombocytopenia (Germeshausen et al. 2006. PubMed ID: 16470591; Jalas et al. 2011. PubMed ID: 21489838). The c.79+2T>A variant has also been characterized as a founder variant in the Ashkenazi Jewish population, being reported in 0.82% of alleles in individuals of Ashkenazi Jewish descent in gnomAD (Jalas et al. 2011. PubMed ID: 21489838). However, it does not occur frequently in other gnomAD populations. Variants that disrupt the consensus splice donor site in MPL are expected to be pathogenic. This variant is interpreted as pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Dec 14, 2018 | The MPL c.79+2T>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The c.79+2T>A variant was identified in a homozygous state in two individuals with congenital amegakaryocytic thrombocytopenia (CAMT) and in a heterozygous state in the unaffected parents of one of the individuals (Germeshausen et al. 2006; Jalas et al. 2011). The variant has not been reported in the literature in association with autosomal dominant essential thrombocythemia. The c.79+2T>A variant was absent from 50 control individuals but is reported at a frequency of 0.00057 in the European (non-Finnish) population from the Exome Aggregation Consortium. In a study of 2018 randomly selected individuals of Ashkenazi Jewish descent, Jalas et al. (2011) established a carrier frequency for the c.79+2T>A variant of one in 75. Haplotype analysis in this study suggested that the c.79+2T>A variant is a founder variant that is part of a haplotype with two upstream variants, though presence of these upstream variants cannot be assessed by the current test. Based on the evidence and the potential impact of splice donor variants, the c.79+2T>A variant is classified as likely pathogenic for MPL-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
Primary myelofibrosis;C3275998:Thrombocythemia 2;C5882667:Congenital amegakaryocytic thrombocytopenia 1 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 06, 2024 | - - |
Congenital amegakaryocytic thrombocytopenia 1 Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Jul 16, 2023 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with recessive thrombocytopenia, congenital amegakaryocytic (MIM#604498) and dominant thrombocythemia 2, (MIM#601977), respectively (PMID: 28955303, PMID: 26423830). (I) 0108 - This gene is associated with both recessive and dominant disease (OMIM). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0252 - This variant is homozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (100 heterozygotes, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0704 - Another canonical splice variant comparable to the one identified in this case has limited previous evidence for pathogenicity. This variant (c.79+1G>T) has been reported as likely pathogenic (ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic or likely pathogenic, and is described as a founder within the Ashkenazi Jewish population (ClinVar, PMID: 32703794, PMID: 21489838). (SP) 1209 - This variant has been shown to be both maternally and paternally inherited (biallelic, by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Primary myelofibrosis Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | May 23, 2019 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This c.79+2T>A variant has been previously reported as disease-causing in patients with CAMT (congenital amegakaryocytic thrombocytopenia) [PMID 16470591, 21489838] - |
Thrombocytopenia Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | research | NIHR Bioresource Rare Diseases, University of Cambridge | Feb 01, 2019 | - - |
Essential thrombocythemia;C1327915:Congenital amegakaryocytic thrombocytopenia Pathogenic:1
| Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2025 | This sequence change affects a donor splice site in intron 1 of the MPL gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in MPL are known to be pathogenic (PMID: 8073287, 11133753). This variant is present in population databases (rs146249964, gnomAD 0.8%). Disruption of this splice site has been observed in individual(s) with congenital amegakaryocytic thrombocytopenia (PMID: 16470591, 21489838). It is commonly reported in individuals of Ashkenazi Jewish ancestry (PMID: 21489838). ClinVar contains an entry for this variant (Variation ID: 135563). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
not specified Other:1
| not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
GERP RS
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dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at