chrX-70445397-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021120.4(DLG3):c.196A>C(p.Thr66Pro) 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 benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T66I) has been classified as Likely benign.
Frequency
Consequence
NM_021120.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLG3 | NM_021120.4 | c.196A>C | p.Thr66Pro | missense_variant | 1/19 | ENST00000374360.8 | |
DLG3 | XM_006724625.3 | c.196A>C | p.Thr66Pro | missense_variant | 1/20 | ||
DLG3 | XM_011530883.2 | c.196A>C | p.Thr66Pro | missense_variant | 1/19 | ||
DLG3 | XM_006724626.3 | c.196A>C | p.Thr66Pro | missense_variant | 1/20 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLG3 | ENST00000374360.8 | c.196A>C | p.Thr66Pro | missense_variant | 1/19 | 1 | NM_021120.4 | ||
DLG3 | ENST00000194900.8 | c.196A>C | p.Thr66Pro | missense_variant | 1/21 | 5 | P1 | ||
DLG3 | ENST00000463252.5 | n.262A>C | non_coding_transcript_exon_variant | 1/19 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 111995Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315 FAILED QC
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 111995Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34315
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.196A>C (p.T66P) alteration is located in exon 1 (coding exon 1) of the DLG3 gene. This alteration results from a A to C substitution at nucleotide position 196, causing the threonine (T) at amino acid position 66 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.