ClinVar Miner

Submissions for variant NM_006096.3(NDRG1):c.1053_1082del (p.340_349TRSRSHTSEG[2]) (rs751274009)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000792340 SCV000931629 uncertain significance Charcot-Marie-Tooth disease type 4 2019-12-24 criteria provided, single submitter clinical testing This variant, c.1053_1082del, results in the deletion of 10 amino acids of the NDRG1 protein (p.Thr360_Gly369del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with NDRG1-related disease. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
CeGaT Praxis fuer Humangenetik Tuebingen RCV000999079 SCV001155490 uncertain significance not provided 2019-02-01 criteria provided, single submitter clinical testing
Molecular Genetics Laboratory,London Health Sciences Centre RCV001174338 SCV001337474 likely benign Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001286510 SCV001473096 likely benign Charcot-Marie-Tooth disease, type 4D 2020-05-07 criteria provided, single submitter clinical testing
Natera, Inc. RCV000792340 SCV001462044 uncertain significance Charcot-Marie-Tooth disease type 4 2020-09-16 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000999079 SCV001551018 uncertain significance not provided no assertion criteria provided clinical testing The NDRG1 p.Thr294_Gly303del variant was not identified in the literature but was identified in dbSNP (ID: rs751274009) and ClinVar (classified as uncertain significance by Invitae and CeGaT Praxis fuer Humangenetik Tuebingen). The variant was identified in control databases in 96 of 241916 chromosomes (1 homozygous) at a frequency of 0.0003968 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: African in 28 of 21222 chromosomes (freq: 0.001319), South Asian in 17 of 26616 chromosomes (freq: 0.000639), East Asian in 10 of 17388 chromosomes (freq: 0.000575), Latino in 9 of 31000 chromosomes (freq: 0.00029), European (non-Finnish) in 31 of 109262 chromosomes (freq: 0.000284) and Other in 1 of 6306 chromosomes (freq: 0.000159), but was not observed in the Ashkenazi Jewish or European (Finnish) populations. This variant is an in-frame deletion; the impact of this alteration on NDRG1 protein function is not known. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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