rs1553648931
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000030.3(AGXT):c.680+480_776+69delinsTGAGA variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron 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
Genomes: not found (cov: 34)
Consequence
AGXT
NM_000030.3 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_000030.3 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.997
Genes affected
AGXT (HGNC:341): (alanine--glyoxylate aminotransferase) This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-240874542-CCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTC-TGAGA is Pathogenic according to our data. Variant chr2-240874542-CCTGGCAACTGGAGGTGCCGTTCCCCAGAACAGAGAGGACTTCGGGGAGAAGTCAGGAATTCGGTGTTGGACGTGGGAGGTCTGAGATGCCAGCTGGACCACACGGGAGGGTGAAGGAAGCGGCTGGGTGTGAGTCAGGAGCCTGGGGAGAGGCCGGGGCTGGCCCCTCCATCTGGAGTTGTAGAGACGGACACATTTAAAGTTTCAAGCCTGGCCAGTGTCCCCTGGGGCCCGAAAGCAGTCACCTTTGGGTGATGTGAGAAATGAAGGCTGACCCTGTAGGAGGGGCTGGGGGAGAGAAAGGGGCACACAGAGTGGAGGGAGCTGGCCTTGGTGCCCCCATGGCAGGGTCACACAGCTGGGCCCAAGGGCCAGCGGGACTGGACAGCTGAGGGACCCACGACCCACCCGGTCCCACTCTGGCCCCTGAGCACAAATGCAGCTGGGGCGGGCCCTCCTGGGGGCCCCACCCCGTCTCACTCCCGTGAAACAGGACAGCCAGCGAGACTGCCCTGGCCTTCAGCCCAAACTGAGAGGCTGGTGCTCAGCCTGCTTCTTTCTCCCCAGAAAGAAGATGTACTCCCGCAAGACGAAGCCCTTCTCCTTCTACCTGGACATCAAGTGGCTGGCCAACTTCTGGGGCTGTGACGACCAGCCCAGGATGTGAGGCCTGGCAGGGATGGGAAGGTGGAGGGCGCTGGGCATGGCTGAGAGGTGGGGCGCTGGCCTCTC-TGAGA is described in ClinVar as [Pathogenic]. Clinvar id is 204196.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGXT | NM_000030.3 | c.680+480_776+69delinsTGAGA | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 7/11 | ENST00000307503.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGXT | ENST00000307503.4 | c.680+480_776+69delinsTGAGA | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 7/11 | 1 | NM_000030.3 | P1 | ||
AGXT | ENST00000476698.1 | n.333-567_428+69delinsTGAGA | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, non_coding_transcript_exon_variant, intron_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD3 genomes
Cov.:
34
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 34
GnomAD4 genome
Cov.:
34
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary hyperoxaluria, type I Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Thalassemia Center, San Luigi University Hospital | Oct 27, 2023 | ACMG:PVS1 PM1 PM2 PM4 - |
Pathogenic, no assertion criteria provided | research | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at