Submissions for variant NM_014844.5(TECPR2):c.1944_1947del (p.Thr649fs)

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Total submissions: 4

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Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV001008078	SCV001167816	likely pathogenic	not provided	2019-02-08	criteria provided, single submitter	clinical testing	The c.1944_1947delCACT variant in the TECPR2 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1944_1947delCACT variant causes a frameshift starting with codon Threonine 649, changes this amino acid to a Cysteine residue, and creates a premature Stop codon at position 35 of the new reading frame, denoted p.Thr649CysfsX35. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1944_1947delCACT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.1944_1947delCACT as a likely pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001836063	SCV002961646	pathogenic	Hereditary spastic paraplegia 49	2023-05-13	criteria provided, single submitter	clinical testing	ClinVar contains an entry for this variant (Variation ID: 817027). This sequence change creates a premature translational stop signal (p.Thr649Cysfs*35) in the TECPR2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TECPR2 are known to be pathogenic (PMID: 23176824, 25590979). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TECPR2-related conditions. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV001836063	SCV005637429	likely pathogenic	Hereditary spastic paraplegia 49	2024-04-07	criteria provided, single submitter	clinical testing
Natera, Inc.	RCV001836063	SCV002091120	likely pathogenic	Hereditary spastic paraplegia 49	2020-08-14	no assertion criteria provided	clinical testing

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