NM_000051.4:c.2572_2574delTTTinsA

Variant names:

• chr11-108267276-TTT-A
• rs587778068
• NM_000051.4:c.2572_2574delTTTinsA

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000051.4(ATM):​c.2572_2574delTTTinsA​(p.Phe858LysfsTer5) variant causes a frameshift, missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F858L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ATM NM_000051.4 frameshift, missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 2.94
• Publications: 0 publications found

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]

ATM Gene-Disease associations (from GenCC):

• hereditary breast carcinoma

  Inheritance: AD Classification: DEFINITIVE Submitted by: Ambry Genetics, ClinGen
• ataxia telangiectasia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), G2P, ClinGen, Laboratory for Molecular Medicine, Orphanet
• hereditary nonpolyposis colon cancer

  Inheritance: AD Classification: MODERATE, LIMITED Submitted by: ClinGen, Ambry Genetics
• prostate cancer

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• familial ovarian cancer

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• gastric carcinoma

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 12 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 11-108267276-TTT-A is Pathogenic according to our data. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-108267276-TTT-A is described in CliVar as Pathogenic. Clinvar id is 1793256.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ATM	NM_000051.4	c.2572_2574delTTTinsA	p.Phe858LysfsTer5	frameshift_variant, missense_variant	Exon 17 of 63	ENST00000675843.1	NP_000042.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ATM	ENST00000675843.1	c.2572_2574delTTTinsA	p.Phe858LysfsTer5	frameshift_variant, missense_variant	Exon 17 of 63		NM_000051.4	ENSP00000501606.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1

Nov 16, 2020

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.2572_2574delTTTinsA pathogenic mutation, located in coding exon 16 of the ATM gene, results from the deletion of 3 nucleotides and insertion of one nucleotide causing a translational frameshift with a predicted alternate stop codon (p.F858Kfs*5). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs587778068; hg19: chr11-108138003;