ClinVar Miner

Submissions for variant NM_001039213.4(CEACAM16):c.703C>T (p.Arg235Cys)

gnomAD frequency: 0.00004  dbSNP: rs746164064
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV001288903 SCV001476309 uncertain significance not provided 2020-03-26 criteria provided, single submitter clinical testing
Invitae RCV001288903 SCV002233019 pathogenic not provided 2023-12-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 235 of the CEACAM16 protein (p.Arg235Cys). This variant is present in population databases (rs746164064, gnomAD 0.02%). This missense change has been observed in individuals with autosomal recessive deafness (PMID: 33111345). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 236048). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. For these reasons, this variant has been classified as Pathogenic.
3billion RCV002283470 SCV002573307 pathogenic Hearing loss, autosomal recessive 113 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: 0.014%). Missense changes are a common disease-causing mechanism. It has been previously reported to be associated with CEACAM16-related disorder (ClinVar ID: VCV000236048 / PMID: 33111345 / 3billion dataset). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID: 33111345). The variant has been reported to co-segregate with the disease in at least 5 similarly affected relatives/individuals in the same family or similarly affected unrelated family (PMID: 33111345). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.
GeneDx RCV001288903 SCV002586727 uncertain significance not provided 2022-04-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33111345, 35118517)
Laboratory of Prof. Karen Avraham, Tel Aviv University RCV000225009 SCV000281995 pathogenic Nonsyndromic genetic hearing loss 2016-02-16 no assertion criteria provided research Teenage onset, mild-moderate HL

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