ClinVar Miner

Submissions for variant NM_004715.5(CTDP1):c.440C>T (p.Thr147Met)

gnomAD frequency: 0.00002  dbSNP: rs143464787
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000444161 SCV000535664 uncertain significance not provided 2019-11-25 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Neuberg Centre For Genomic Medicine, NCGM RCV002510574 SCV002820140 uncertain significance Congenital cataracts-facial dysmorphism-neuropathy syndrome criteria provided, single submitter clinical testing The missense variant p.T147M in CTDP1 (NM_004715.4) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. It has been reported as a variant of uncertain significance in the ClinVar database. It is novel (not in any individuals) in gnomAD ExomesThe p.T147M variant is novel (not in any individuals) in 1000 Genomes. There is a moderate physicochemical difference between threonine and methionine. The p.T147M missense variant is predicted to be damaging by both SIFT and PolyPhen2. The threonine residue at codon 147 of CTDP1 is conserved in all mammalian species. The nucleotide c.440 in CTDP1 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV000444161 SCV003510877 uncertain significance not provided 2021-12-03 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 147 of the CTDP1 protein (p.Thr147Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CTDP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 392399). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
Ambry Genetics RCV004022511 SCV004851044 uncertain significance not specified 2024-01-09 criteria provided, single submitter clinical testing The c.440C>T (p.T147M) alteration is located in exon 3 (coding exon 3) of the CTDP1 gene. This alteration results from a C to T substitution at nucleotide position 440, causing the threonine (T) at amino acid position 147 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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