ClinVar Miner

Submissions for variant NM_033517.1(SHANK3):c.3424_3425del (p.Leu1142fs) (rs1555910143)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000413185 SCV000491111 pathogenic not provided 2018-02-16 criteria provided, single submitter clinical testing The c.3424_3425delCT variant in the SHANK3 gene has been reported previously as a heterozygous de novo pathogenic variant in an individual with neonatal hypotonia, global developmental delay, regression, severe intellectual disability, non-verbal autism, and typical Phelan-McDermid dysmorphic facies (Leblond et al., 2014). The c.3424_3425delCT variant causes a frameshift starting with codon Leucine 1142, changes this amino acid to a Valine residue, and creates a premature Stop codon at position 153 of the new reading frame, denoted p.Leu1142ValfsX153. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3424_3425delCT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.3424_3425delCT as a pathogenic variant.
Liping Wei Laboratory,Peking University RCV000754674 SCV000804766 pathogenic Autism spectrum disorder 2018-08-01 criteria provided, single submitter research
Mendelics RCV000990465 SCV001141465 likely pathogenic 22q13.3 deletion syndrome 2019-05-28 criteria provided, single submitter clinical testing
GenomeConnect, ClinGen RCV000509224 SCV000606928 not provided SHANK3-Related Disorder no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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