9-85588359-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001330701.2(AGTPBP1):c.2842C>T(p.Arg948Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000248 in 1,611,434 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 (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
AGTPBP1
NM_001330701.2 stop_gained
NM_001330701.2 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 5.23
Genes affected
AGTPBP1 (HGNC:17258): (ATP/GTP binding carboxypeptidase 1) NNA1 is a zinc carboxypeptidase that contains nuclear localization signals and an ATP/GTP-binding motif that was initially cloned from regenerating spinal cord neurons of the mouse.[supplied by OMIM, Jul 2002]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 9-85588359-G-A is Pathogenic according to our data. Variant chr9-85588359-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 599381.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTPBP1 | NM_001330701.2 | c.2842C>T | p.Arg948Ter | stop_gained | 21/26 | ENST00000357081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTPBP1 | ENST00000357081.8 | c.2842C>T | p.Arg948Ter | stop_gained | 21/26 | 5 | NM_001330701.2 | P1 | |
AGTPBP1 | ENST00000376083.7 | c.2722C>T | p.Arg908Ter | stop_gained | 21/26 | 1 | |||
AGTPBP1 | ENST00000337006.8 | c.2998C>T | p.Arg1000Ter | stop_gained | 20/25 | 5 | |||
AGTPBP1 | ENST00000628899.1 | c.2878C>T | p.Arg960Ter | stop_gained | 20/25 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459412Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726014
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GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74228
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Global developmental delay;C3279222:Aplasia/Hypoplasia of the cerebellum Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Hadassah Hebrew University Medical Center | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
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BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A;A;D;D
Vest4
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at