Submissions for variant NM_001042492.3(NF1):c.5030TCTATA[1] (p.Ile1679_Tyr1680del)

dbSNP: rs1135402868

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000680826	SCV000808274	pathogenic	not provided	2022-11-03	criteria provided, single submitter	clinical testing	In-frame deletion of 2 amino acids in a non-repeat region; Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31121919, 10534774, 30530636, 21089070, 31370276, 31776437)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000497071	SCV000817609	pathogenic	Neurofibromatosis, type 1	2024-12-12	criteria provided, single submitter	clinical testing	This variant, c.4973_4978del, results in the deletion of 2 amino acid(s) of the NF1 protein (p.Ile1658_Tyr1659del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with neurofibromatosis type 1 (PMID: 10534774, 30530636; internal data). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 431651). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic.
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV000497071	SCV001478999	likely pathogenic	Neurofibromatosis, type 1	2020-10-26	criteria provided, single submitter	clinical testing
Revvity Omics, Revvity	RCV000680826	SCV002020113	likely pathogenic	not provided	2021-08-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000497071	SCV002560099	pathogenic	Neurofibromatosis, type 1	2022-03-15	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002341172	SCV002643984	pathogenic	Hereditary cancer-predisposing syndrome; Cardiovascular phenotype	2022-02-17	criteria provided, single submitter	clinical testing	The c.4973_4978delTCTATA pathogenic mutation (also known as p.I1658_Y1659del) is located in coding exon 36 of the NF1 gene. This pathogenic mutation results from an in-frame TCTATA deletion at nucleotide positions 4973 to 4978. This results in the in-frame deletion of isoleucine and tyrosine at amino acid positions 1658 and 1659. This variant has been determined to be the result of a de novo mutation or germline mosaicism in one individual with NF1 (Ambry internal data). This variant has also been observed in literature in multiple individuals and families with clinical diagnosis of NF1 (Wu R et al. Genes Chromosomes Cancer 1999;26(4):376-80); (Giugliano T et al. Genes (Basel), 2019 07;10:); (Maani N et al. Cancers (Basel), 2019 May;11:); (Kang E et al. J Hum Genet, 2020 Jan;65:79-89). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). This amino acid region is well conserved in available vertebrate species. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000680826	SCV003800060	likely pathogenic	not provided	2022-04-04	criteria provided, single submitter	clinical testing	The NF1 c.5036_5041delTCTATA; p.Ile1679_Tyr1680del variant (rs1135402868), also known as 4973delTCTATA for NM_000267.3, is reported in the literature in multiple individuals with NF1 (Frayling 2019, Giugliano 2019, Maani 2019, Wu 1999), and is reported in ClinVar (Variation ID: 431651). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant deletes an isoleucine and tyrosine residue leaving the rest of the protein in-frame. Based on available information, this variant is considered to be likely pathogenic. References: Frayling IM et al. Breast cancer risk in neurofibromatosis type 1 is a function of the type of NF1 gene mutation: a new genotype-phenotype correlation. J Med Genet. 2019 Apr;56(4):209-219. PMID: 30530636. Giugliano T et al. Clinical and Genetic Findings in Children with Neurofibromatosis Type 1, Legius Syndrome, and Other Related Neurocutaneous Disorders. Genes (Basel). 2019 Jul 31;10(8):580. PMID: 31370276. Maani N et al. NF1 Patients Receiving Breast Cancer Screening: Insights from The Ontario High Risk Breast Screening Program. Cancers (Basel). 2019 May 22;11(5):707. PMID: 31121919. Wu R et al. Germline mutations in NF1 patients with malignancies. Genes Chromosomes Cancer. 1999 Dec;26(4):376-80. PMID: 10534774.
Baylor Genetics	RCV003464066	SCV004198404	pathogenic	Juvenile myelomonocytic leukemia	2023-07-23	criteria provided, single submitter	clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	RCV000497071	SCV004543807	likely pathogenic	Neurofibromatosis, type 1	2024-02-14	criteria provided, single submitter	clinical testing
Medical Genetics, University of Parma	RCV000497071	SCV000588795	pathogenic	Neurofibromatosis, type 1	2017-02-02	no assertion criteria provided	clinical testing