2-3604419-CCGGCTGGCGATGA-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_024027.5(COLEC11):c.82_94delGCTGGCGATGACG(p.Ala28ProfsTer69) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_024027.5 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
3MC syndrome Pathogenic:1
This sequence change in COLEC11 is a frameshift variant predicted to cause a premature stop codon, p.(Ala28Profs*69), in biologically relevant exon 5/7 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism. This variant is absent from the population database gnomAD v2.1 and v3.1. This variant has been detected homozygous in at least one individual with 3MC syndrome (Kulak et al, https://motto.tc/siteler/www.cocukgenetik2019.com/cocuk-genetik-bildiri-kitabi.pdf). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as PATHOGENIC. Following criteria are met: PVS1, PM2_Supporting, PM3_Supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.