ClinVar Miner

Submissions for variant NM_005199.5(CHRNG):c.1012T>C (p.Ser338Pro)

gnomAD frequency: 0.00008  dbSNP: rs776733115
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV002486476 SCV002775344 uncertain significance Autosomal recessive multiple pterygium syndrome; Lethal multiple pterygium syndrome 2022-03-02 criteria provided, single submitter clinical testing
Ambry Genetics RCV002547599 SCV003688473 uncertain significance Inborn genetic diseases 2022-11-30 criteria provided, single submitter clinical testing The c.1012T>C (p.S338P) alteration is located in exon 9 (coding exon 9) of the CHRNG gene. This alteration results from a T to C substitution at nucleotide position 1012, causing the serine (S) at amino acid position 338 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001354962 SCV001549697 uncertain significance not provided no assertion criteria provided clinical testing The CHRNG p.Ser338Pro variant was not identified in the literature nor was it identified in ClinVar, Cosmic, or LOVD 3.0. The variant was identified in dbSNP (ID: rs776733115) and in control databases in 24 of 282666 chromosomes at a frequency of 0.000085 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 23 of 129076 chromosomes (freq: 0.000178) and Other in 1 of 7220 chromosomes (freq: 0.000139); it was not observed in the African, Latino, Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Ser338 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, and MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. 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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