rs587781946

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate

The NM_000051.4(ATM):ā€‹c.8187A>Cā€‹(p.Gln2729His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,762 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 Uncertain significance (ā˜…ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000096 ( 0 hom. )

Consequence

ATM
NM_000051.4 missense

Scores

9
8
2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:8

Conservation

PhyloP100: 2.81
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]
C11orf65 (HGNC:28519): (chromosome 11 open reading frame 65) Predicted to be involved in negative regulation of mitochondrial fission and negative regulation of protein targeting to mitochondrion. Predicted to be located in cytosol and mitochondrial outer membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PP3
MetaRNN computational evidence supports a deleterious effect, 0.932

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATMNM_000051.4 linkuse as main transcriptc.8187A>C p.Gln2729His missense_variant 56/63 ENST00000675843.1 NP_000042.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATMENST00000675843.1 linkuse as main transcriptc.8187A>C p.Gln2729His missense_variant 56/63 NM_000051.4 ENSP00000501606 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.0000159
AC:
4
AN:
251036
Hom.:
0
AF XY:
0.0000221
AC XY:
3
AN XY:
135670
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000353
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000958
AC:
14
AN:
1461762
Hom.:
0
Cov.:
30
AF XY:
0.00000688
AC XY:
5
AN XY:
727186
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:
0.0000126
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.0000330
AC:
4

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Ataxia-telangiectasia syndrome Uncertain:3
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 09, 2024This sequence change replaces glutamine, which is neutral and polar, with histidine, which is basic and polar, at codon 2729 of the ATM protein (p.Gln2729His). This variant is present in population databases (rs587781946, gnomAD 0.004%). This missense change has been observed in individual(s) with breast cancer and/or prostate cancer (PMID: 24556621, 29335925, 35127508, 35264596, 35534704). ClinVar contains an entry for this variant (Variation ID: 141700). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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. -
Uncertain significance, criteria provided, single submitterclinical testingMendelicsJul 02, 2018- -
Uncertain significance, criteria provided, single submitterclinical testingCounsylApr 28, 2017- -
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthJun 22, 2019- -
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMar 22, 2024The p.Q2729H variant (also known as c.8187A>C), located in coding exon 55 of the ATM gene, results from an A to C substitution at nucleotide position 8187. The glutamine at codon 2729 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported in a male patient diagnosed with breast cancer (Fostira F et al. Breast Cancer Res. Treat., 2018 May;169:105-113). This alteration has also been reported in 1/191 men with a personal and family history of prostate cancer (Leongamornlert D et al. Br. J. Cancer, 2014 Mar;110:1663-72). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpOct 31, 2023Variant summary: ATM c.8187A>C (p.Gln2729His) results in a non-conservative amino acid change located in the Phosphatidylinositol 3-/4-kinase, catalytic domain (IPR000403) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.6e-05 in 251036 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.8187A>C has been reported in the literature in individuals with multiple cancer types, without evidence of causality, including breast Cancer (e.g. Guindalini_2022, Andrikopoulou_2021) male breast cancer (e.g. Fostira_2018), prostate cancer (e.g. Leongamornlert_2014, Karlsson_2021), melanoma (e.g. Dalmasso_2021), colorectal cancer (e.g. Randon_2019), chronic lymphocytic leukemia or other hemoatological malignancy (e.g. Lampson_2023), without cancer but with cancer family history (e.g. deOlivera_2022), and conversely, in control cohorts without a cancer phenotype (e.g. Tiao_2015, Karlsson_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Breast Cancer. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 35127508, 34262154, 29335925, 35264596, 33436325, 36315919, 24556621, 30814645, 28652578, 35534704). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxApr 20, 2023Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with breast or prostate cancer (Leongamornlert et al., 2014; Fostira et al., 2018; Andrikopoulou et al., 2022; Guindalini et al., 2022); This variant is associated with the following publications: (PMID: 29678143, 25148578, 24556621, 29335925, 30814645, 35127508, 23532176, 15279808, 35226061, 35264596) -
Familial cancer of breast Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsDec 19, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.33
D
BayesDel_noAF
Pathogenic
0.34
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.42
T;T
Eigen
Uncertain
0.54
Eigen_PC
Uncertain
0.46
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.93
D;.
M_CAP
Pathogenic
0.51
D
MetaRNN
Pathogenic
0.93
D;D
MetaSVM
Pathogenic
0.85
D
MutationAssessor
Pathogenic
3.7
H;H
MutationTaster
Benign
1.0
D;D;D
PrimateAI
Uncertain
0.78
T
PROVEAN
Uncertain
-4.2
D;D
REVEL
Pathogenic
0.87
Sift
Uncertain
0.0010
D;D
Sift4G
Pathogenic
0.0010
D;D
Polyphen
1.0
D;D
Vest4
0.92
MutPred
0.65
Loss of disorder (P = 0.061);Loss of disorder (P = 0.061);
MVP
0.96
MPC
0.56
ClinPred
0.99
D
GERP RS
4.6
Varity_R
0.84
gMVP
0.79

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: rs587781946; hg19: chr11-108206607; COSMIC: COSV53762213; COSMIC: COSV53762213; API