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NM_000051.4(ATM):c.6780A>G (p.Ile2260Met) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
May 6, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001354238.11

Allele description [Variation Report for NM_000051.4(ATM):c.6780A>G (p.Ile2260Met)]

NM_000051.4(ATM):c.6780A>G (p.Ile2260Met)

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.6780A>G (p.Ile2260Met)
HGVS:
  • NC_000011.10:g.108325517A>G
  • NG_009830.1:g.107686A>G
  • NG_054724.1:g.149316T>C
  • NM_000051.4:c.6780A>GMANE SELECT
  • NM_001330368.2:c.641-16446T>C
  • NM_001351110.2:c.*38+9703T>C
  • NM_001351834.2:c.6780A>G
  • NP_000042.3:p.Ile2260Met
  • NP_000042.3:p.Ile2260Met
  • NP_001338763.1:p.Ile2260Met
  • LRG_135t1:c.6780A>G
  • LRG_135:g.107686A>G
  • LRG_135p1:p.Ile2260Met
  • NC_000011.9:g.108196244A>G
  • NM_000051.3:c.6780A>G
Protein change:
I2260M
Links:
dbSNP: rs1555119325
NCBI 1000 Genomes Browser:
rs1555119325
Molecular consequence:
  • NM_001330368.2:c.641-16446T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+9703T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.6780A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.6780A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001548800Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

SCV001778043GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Uncertain significance
(May 6, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001548800.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The ATM p.Ile2260Met variant was not identified in the literature nor was it identified in the dbSNP, ClinVar, Genesight-COGR, Cosmic, MutDB, and LOVD 3.0 databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, and the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Ile2260 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV001778043.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 13, 2024