9-85579069-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001330701.2(AGTPBP1):​c.3193G>A​(p.Ala1065Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000436 in 1,607,116 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )

Consequence

AGTPBP1
NM_001330701.2 missense

Scores

3
9
7

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.14
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AGTPBP1NM_001330701.2 linkc.3193G>A p.Ala1065Thr missense_variant Exon 24 of 26 ENST00000357081.8 NP_001317630.1 Q9UPW5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AGTPBP1ENST00000357081.8 linkc.3193G>A p.Ala1065Thr missense_variant Exon 24 of 26 5 NM_001330701.2 ENSP00000349592.3 Q9UPW5-1

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
151900
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000412
AC:
6
AN:
1455216
Hom.:
0
Cov.:
30
AF XY:
0.00000691
AC XY:
5
AN XY:
723922
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000451
Gnomad4 OTH exome
AF:
0.0000167
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
151900
Hom.:
0
Cov.:
33
AF XY:
0.0000135
AC XY:
1
AN XY:
74176
show subpopulations
Gnomad4 AFR
AF:
0.0000242
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Inborn genetic diseases Uncertain:1
Mar 08, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.3073G>A (p.A1025T) alteration is located in exon 24 (coding exon 23) of the AGTPBP1 gene. This alteration results from a G to A substitution at nucleotide position 3073, causing the alanine (A) at amino acid position 1025 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.72
BayesDel_addAF
Uncertain
0.048
T
BayesDel_noAF
Benign
-0.17
CADD
Pathogenic
30
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.25
.;.;T;.
Eigen
Uncertain
0.47
Eigen_PC
Uncertain
0.54
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.97
D;D;D;D
M_CAP
Benign
0.018
T
MetaRNN
Uncertain
0.52
D;D;D;D
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.7
.;.;L;.
PrimateAI
Uncertain
0.59
T
PROVEAN
Uncertain
-2.9
D;.;D;.
REVEL
Benign
0.17
Sift
Uncertain
0.0040
D;.;D;.
Sift4G
Uncertain
0.010
D;D;D;D
Polyphen
0.87
P;.;D;B
Vest4
0.68
MVP
0.50
MPC
1.5
ClinPred
0.99
D
GERP RS
4.6
Varity_R
0.40
gMVP
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs375377783; hg19: chr9-88193984; API