chr9-85588449-G-A
Position:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_ModeratePP5_Moderate
The NM_001330701.2(AGTPBP1):c.2752C>T(p.Arg918Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,459,148 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 (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
AGTPBP1
NM_001330701.2 missense
NM_001330701.2 missense
Scores
12
2
3
Clinical Significance
Conservation
PhyloP100: 5.22
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 Likely_pathogenic. Variant got 6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.914
PP5
Variant 9-85588449-G-A is Pathogenic according to our data. Variant chr9-85588449-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 599369.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGTPBP1 | NM_001330701.2 | c.2752C>T | p.Arg918Trp | missense_variant | 21/26 | ENST00000357081.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGTPBP1 | ENST00000357081.8 | c.2752C>T | p.Arg918Trp | missense_variant | 21/26 | 5 | NM_001330701.2 | P1 | |
AGTPBP1 | ENST00000376083.7 | c.2632C>T | p.Arg878Trp | missense_variant | 21/26 | 1 | |||
AGTPBP1 | ENST00000337006.8 | c.2908C>T | p.Arg970Trp | missense_variant | 20/25 | 5 | |||
AGTPBP1 | ENST00000628899.1 | c.2788C>T | p.Arg930Trp | missense_variant | 20/25 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459148Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725820
GnomAD4 exome
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2
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1459148
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30
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1
AN XY:
725820
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Bravo
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neurodegeneration, childhood-onset, with cerebellar atrophy Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 14, 2019 | - - |
Pathogenic, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Mar 14, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;.;D;.
REVEL
Uncertain
Sift
Pathogenic
D;.;D;.
Sift4G
Pathogenic
D;D;D;D
Polyphen
D;.;D;D
Vest4
MutPred
0.77
.;.;Gain of catalytic residue at P921 (P = 0.0237);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AL_spliceai
Position offset: 29
Find out detailed SpliceAI scores and Pangolin per-transcript scores at