chr6-21594732-C-A
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP3_StrongPP5_Moderate
The NM_003107.3(SOX4):c.198C>A(p.Phe66Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_003107.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1443688Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 716158
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, mild Pathogenic:1
The p.Phe66Leu variant is de novo, it is absent in population databases and it involves a higly conserved residue in the HMG box DNA-binding domain of the protein. Three further patients were identified with de novo missense variants affecting the HMG box DNA-binding domain of SOX4. Intellectual disability and similar facial dysmorphisms were present in all four. Functional assays demonstrated that SOX4 proteins carrying these four variants are unable to bind DNA in vitro and transactivate SOX reporter genes in cultured cells. -
Coffin-Siris syndrome 10 Pathogenic:1
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Developmental delay;C3714756:Intellectual disability;na:Mild facial and digital morphological abnormalities Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at