chr2-10440781-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_002539.3(ODC1):c.1329G>A(p.Trp443*) variant causes a stop gained 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_002539.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ODC1 | NM_002539.3 | c.1329G>A | p.Trp443* | stop_gained | Exon 12 of 12 | ENST00000234111.9 | NP_002530.1 | |
ODC1 | NM_001287189.2 | c.1329G>A | p.Trp443* | stop_gained | Exon 12 of 12 | NP_001274118.1 | ||
ODC1 | NM_001287190.2 | c.1329G>A | p.Trp443* | stop_gained | Exon 12 of 12 | NP_001274119.1 | ||
ODC1 | NM_001287188.2 | c.942G>A | p.Trp314* | stop_gained | Exon 12 of 12 | NP_001274117.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with alopecia and brain abnormalities Pathogenic:1
The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Stop-gained (nonsense): predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.