chr5-140114183-T-TGGCG
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate
The NM_005859.5(PURA):c.4_7dup(p.Asp3?) variant causes a frameshift, start lost change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. MADRDSGSEQGGAALGSGGSLGHPGSGSGSGGGGGGGGGGGGSGGGGGGAPGGLQHETQELASKRVDIQNKRFYLDVKQNAKGRFLKI1?) has been classified as Pathogenic.
Frequency
Consequence
NM_005859.5 frameshift, start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PURA | NM_005859.5 | c.4_7dup | p.Asp3? | frameshift_variant, start_lost | 1/1 | ENST00000331327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PURA | ENST00000331327.5 | c.4_7dup | p.Asp3? | frameshift_variant, start_lost | 1/1 | NM_005859.5 | P1 | ||
PURA | ENST00000502351.1 | c.4_7dup | p.Asp3? | frameshift_variant, start_lost | 2/2 | 2 | |||
PURA | ENST00000505703.2 | c.4_7dup | p.Asp3? | frameshift_variant, start_lost | 2/2 | 3 | |||
PURA | ENST00000651386.1 | c.4_7dup | p.Asp3? | frameshift_variant, start_lost | 2/2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 9
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.