chr5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The 5-140113537-CGCATGAGAGGGGGTGGCCGTGACTCGGTGTCCCCTCTTTGCAGGGGGCTCTGCTGCGCCGCGCAGGCCCCTCCTCCTACATCCTCTTTGGGGGGTCACTGGAAAGCAGAGCTTAGGCCCACTCTCTGTGCTTAGTATGGCAGACTCCTTCTCACCCCTAGTCCCCTAACTCCCCAGGCCGAGGCCGCCTAGGGTCTGCCCAACAGCGACAGCCACGGTGGTGGTGGTGGTGGTGGTGGTGGTAGCAGTGGTGGCGGCAGCAGCGGCAGCAGCAGCTGCGACGCTGCGCGTCCTGCTCCCTCTCCCCCACCCAGCCAGGGTTGTAGGGTGAGGGCCGGTGGGTGGGCGCCGCCTGGCGGGCGGGCGGACGGGGGGCTGGCAGCGGGGAGGGGGCGCAGGTCACGTGCCGGCGGGCGGGTGGGCGCGTACAGTAGGGCGCCCTGCTACTGTACTGGGGAGTCAGTGCCCTGTTACCGGGTCTCGTCTGTCTCGTCTCTCCCGCAGATCTCGCGAGAGTGGCTGACTGGCTGTGGGGGTTGCGGCGGCAGCAGGCGGAGCCGGGGAGGGAAAGCAGCGGCGGCTGAGGCGACTGAGGCGGCGGGCGGAGCGGCAGGCGGCGGCGGCGCGGCAGCGGAGCGCAGCATCATGGCGGACCGAGACAGCGGCAGCGAGCAGGGTGGTGCGGCGCTGGGTTCGGGCGGCTCCCTGGGGCACCCCGGCTCGGGCTCAGGCTCCGGCGGGGGCGGTGGTGGCGGCGGGGGCGGCGGCGGCAGTGGCGGCGGCGGCGGCGGGGCCCCAGGGGGGCTGCAGCACGAGACGCAGGAGCTGGCCTCCAAGCGGGTGGACATCCAGAACAAGCGCTTCTACCTGGACGTGAAGCAGAACGCCAAGGGCCGCTTCCTGAAGAT-GAGGTGGG variant causes a coding sequence, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_005859.5 coding_sequence, 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PURA | NM_005859.5 | coding_sequence_variant, 5_prime_UTR_variant | 1/1 | ENST00000331327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PURA | ENST00000331327.5 | coding_sequence_variant, 5_prime_UTR_variant | 1/1 | NM_005859.5 | P1 | ||||
PURA | ENST00000502351.1 | splice_acceptor_variant, coding_sequence_variant, 5_prime_UTR_variant, 3_prime_UTR_variant, intron_variant | 2/2 | 2 | |||||
PURA | ENST00000505703.2 | c.-141-504_263delinsGAGGTGGG | splice_acceptor_variant, coding_sequence_variant, 5_prime_UTR_variant, intron_variant | 2/2 | 3 | ||||
PURA | ENST00000651386.1 | c.-141-504_263delinsGAGGTGGG | splice_acceptor_variant, coding_sequence_variant, 5_prime_UTR_variant, intron_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 04, 2023 | For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PURA-related conditions. This variant results in the deletion of part of exon 1 (c.-645_263delinsGAGGTGGG) of the PURA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PURA are known to be pathogenic (PMID: 29097605). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.