ClinVar Miner

Submissions for variant NM_004373.4(COX6A1):c.247-7_247-3del

dbSNP: rs587777783
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001857493 SCV002228255 pathogenic not provided 2023-11-14 criteria provided, single submitter clinical testing This sequence change falls in intron 2 of the COX6A1 gene. It does not directly change the encoded amino acid sequence of the COX6A1 protein. This variant is present in population databases (rs587777783, gnomAD 0.02%). This variant has been observed in individuals with Charcot-Marie-Tooth disease (PMID: 25152455, 26302975; Invitae). It has also been observed to segregate with disease in related individuals. This variant is also known as c.247-10_247-6delCACTC. ClinVar contains an entry for this variant (Variation ID: 156370). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
3billion RCV000144453 SCV002573211 pathogenic Charcot-Marie-Tooth disease recessive intermediate D 2022-09-01 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.004%). Intron variant: previously reported to alter splicing and result in a loss of normal protein fucnction through nonsense-mediated decay (NMD) or protein truncation (ClinVar ID:. RCV000678469. / PMID:. 25152455. Predicted Consequence/Location:). The variant has been reported to co-segregate with the disease in at least one similarly affected relative/individual in the same family or similarly affected unrelated family (PMID: 25152455). The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000156370 / PMID: 25152455 , 26302975). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
Baylor Genetics RCV000144453 SCV003835141 pathogenic Charcot-Marie-Tooth disease recessive intermediate D 2021-06-30 criteria provided, single submitter clinical testing
OMIM RCV000144453 SCV000189520 pathogenic Charcot-Marie-Tooth disease recessive intermediate D 2014-09-04 no assertion criteria provided literature only
Genomics England Pilot Project, Genomics England RCV000144453 SCV001760298 likely pathogenic Charcot-Marie-Tooth disease recessive intermediate D no assertion criteria provided clinical testing

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