chr9-85588368-G-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001330701.2(AGTPBP1):c.2833C>T(p.Gln945Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000137 in 1,461,206 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 Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001330701.2 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 |
---|---|---|---|---|---|---|---|
AGTPBP1 | NM_001330701.2 | c.2833C>T | p.Gln945Ter | stop_gained | 21/26 | ENST00000357081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTPBP1 | ENST00000357081.8 | c.2833C>T | p.Gln945Ter | stop_gained | 21/26 | 5 | NM_001330701.2 | P1 | |
AGTPBP1 | ENST00000376083.7 | c.2713C>T | p.Gln905Ter | stop_gained | 21/26 | 1 | |||
AGTPBP1 | ENST00000337006.8 | c.2989C>T | p.Gln997Ter | stop_gained | 20/25 | 5 | |||
AGTPBP1 | ENST00000628899.1 | c.2869C>T | p.Gln957Ter | stop_gained | 20/25 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461206Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726892
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Neurodegeneration, childhood-onset, with cerebellar atrophy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology | Mar 16, 2023 | The c.2833C>T variant is not present in publicly available population databases like 1000 Genomes, ExAC, EVS, Indian Exome Database or our in-house exome database. The variant has neither been published in literature nor reported to clinical databases like in ClinVar, Human Gene Mutation Database (HGMD) or OMIM, in any affected individuals. In silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome, Franklin etc predicted this variant to be likely deleterious. This variant creates a premature translational stop signal at the 945th amino acid position of the transcript that may either result in translation of a truncated protein or causes nonsense mediated decay of the mRNA. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.