7-107891274-C-G
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000108.5(DLD):c.24C>G(p.Tyr8Ter) 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 Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. Y8Y) has been classified as Likely benign.
Frequency
Consequence
NM_000108.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLD | NM_000108.5 | c.24C>G | p.Tyr8Ter | stop_gained | 1/14 | ENST00000205402.10 | |
DLD | NM_001289751.1 | c.24C>G | p.Tyr8Ter | stop_gained | 1/13 | ||
DLD | NM_001289752.1 | c.24C>G | p.Tyr8Ter | stop_gained | 1/13 | ||
DLD | NM_001289750.1 | c.-125C>G | 5_prime_UTR_variant | 1/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLD | ENST00000205402.10 | c.24C>G | p.Tyr8Ter | stop_gained | 1/14 | 1 | NM_000108.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
Pyruvate dehydrogenase E3 deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2023 | This sequence change creates a premature translational stop signal (p.Tyr8*) in the DLD gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DLD are known to be pathogenic (PMID: 8968745, 9934985). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DLD-related conditions. ClinVar contains an entry for this variant (Variation ID: 1392784). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.