rs772591447

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000051.4(ATM):​c.127C>A​(p.Leu43Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: not found (cov: 33)

Consequence

ATM
NM_000051.4 missense

Scores

2
4
13

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2O:1

Conservation

PhyloP100: 0.728
Variant links:
Genes affected
ATM (HGNC:795): (ATM serine/threonine kinase) The protein encoded by this gene belongs to the PI3/PI4-kinase family. This protein is an important cell cycle checkpoint kinase that phosphorylates; thus, it functions as a regulator of a wide variety of downstream proteins, including tumor suppressor proteins p53 and BRCA1, checkpoint kinase CHK2, checkpoint proteins RAD17 and RAD9, and DNA repair protein NBS1. This protein and the closely related kinase ATR are thought to be master controllers of cell cycle checkpoint signaling pathways that are required for cell response to DNA damage and for genome stability. Mutations in this gene are associated with ataxia telangiectasia, an autosomal recessive disorder. [provided by RefSeq, Aug 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2187343).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATMNM_000051.4 linkuse as main transcriptc.127C>A p.Leu43Ile missense_variant 3/63 ENST00000675843.1 NP_000042.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATMENST00000675843.1 linkuse as main transcriptc.127C>A p.Leu43Ile missense_variant 3/63 NM_000051.4 ENSP00000501606 P1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Ataxia-telangiectasia syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpSep 01, 2021This sequence change replaces leucine with isoleucine at codon 43 of the ATM protein (p.Leu43Ile). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with ATM-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 23, 2019The p.L43I variant (also known as c.127C>A), located in coding exon 2 of the ATM gene, results from a C to A substitution at nucleotide position 127. The leucine at codon 43 is replaced by isoleucine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Ataxia-telangiectasia syndrome;C0006142:Malignant tumor of breast Other:1
not provided, no classification providedphenotyping onlyGenomeConnect - Invitae Patient Insights Network-Variant interpreted as Uncertain significance and reported on 09-01-2018 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.28
BayesDel_addAF
Benign
-0.026
T
BayesDel_noAF
Benign
-0.28
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.059
.;T;T;T;.;T;T;T;T;T;T
Eigen
Benign
0.069
Eigen_PC
Benign
-0.049
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.84
T;T;T;T;T;.;.;.;.;.;T
M_CAP
Benign
0.043
D
MetaRNN
Benign
0.22
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.38
T
MutationAssessor
Uncertain
2.6
.;M;.;.;.;M;.;.;.;.;.
MutationTaster
Benign
0.56
D;D
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.2
N;N;N;N;.;N;.;.;.;.;.
REVEL
Benign
0.13
Sift
Pathogenic
0.0
D;D;D;D;.;D;.;.;.;.;.
Sift4G
Pathogenic
0.0
D;D;D;D;D;D;.;.;.;D;D
Polyphen
1.0, 1.0
.;D;.;.;.;D;D;D;D;D;.
Vest4
0.52, 0.69, 0.50, 0.72
MutPred
0.14
Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);Gain of methylation at K41 (P = 0.0559);
MVP
0.77
MPC
0.61
ClinPred
0.95
D
GERP RS
1.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.16
gMVP
0.28

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs772591447; hg19: chr11-108098557; API