chr5-140114184-G-A
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1PS1_ModeratePM2PP5_Moderate
The NM_005859.5(PURA):c.3G>A(p.Met1?) variant causes a start lost change. The variant allele was found at a frequency of 0.00000157 in 636,866 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. MADRDSGSEQGGAALGSGGSLGHPGSGSGSGGGGGGGGGGGGSGGGGGGAPGGLQHETQELASKRVDIQNKRFYLDVKQNAKGRFLKI1?) has been classified as Pathogenic.
Frequency
Consequence
NM_005859.5 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.3G>A | p.Met1? | start_lost | 1/1 | ENST00000331327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PURA | ENST00000331327.5 | c.3G>A | p.Met1? | start_lost | 1/1 | NM_005859.5 | P1 | ||
PURA | ENST00000651386.1 | c.3G>A | p.Met1? | start_lost | 2/2 | P1 | |||
PURA | ENST00000505703.2 | c.3G>A | p.Met1? | start_lost | 2/2 | 3 | |||
PURA | ENST00000502351.1 | c.3G>A | p.Met1? | start_lost | 2/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000157 AC: 1AN: 636866Hom.: 0 Cov.: 9 AF XY: 0.00000323 AC XY: 1AN XY: 309904
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | May 17, 2022 | This sequence change affects the initiator methionine of the PURA mRNA. The next in-frame methionine is located at codon 104. This variant is not present in population databases (gnomAD no frequency). Disruption of the initiator codon has been observed in individual(s) with clinical features of PURA syndrome (PMID: 27148565, 32337850). In at least one individual the variant was observed to be de novo. 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.