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NM_000051.4(ATM):c.477A>G (p.Ile159Met) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 9, 2014
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:
RCV000165553.2

Allele description [Variation Report for NM_000051.4(ATM):c.477A>G (p.Ile159Met)]

NM_000051.4(ATM):c.477A>G (p.Ile159Met)

Gene:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.477A>G (p.Ile159Met)
HGVS:
  • NC_000011.10:g.108235815A>G
  • NG_009830.1:g.17984A>G
  • NM_000051.4:c.477A>GMANE SELECT
  • NM_001351834.2:c.477A>G
  • NP_000042.3:p.Ile159Met
  • NP_000042.3:p.Ile159Met
  • NP_001338763.1:p.Ile159Met
  • LRG_135t1:c.477A>G
  • LRG_135:g.17984A>G
  • LRG_135p1:p.Ile159Met
  • NC_000011.9:g.108106542A>G
  • NM_000051.3:c.477A>G
  • p.I159M
Protein change:
I159M
Links:
dbSNP: rs786202644
NCBI 1000 Genomes Browser:
rs786202644
Molecular consequence:
  • NM_000051.4:c.477A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.477A>G - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000216285Ambry Genetics
criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)		Uncertain significance
(Sep 9, 2014) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000216285.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The p.I159M variant (also known as c.477A>G), located in coding exon 4 of the ATM gene, results from an A to G substitution at nucleotide position 477. The isoleucine at codon 159 is replaced by methionine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6499 samples (12998 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.004% (greater than 22000 alleles tested) in our clinical cohort. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be possibly damaging and deleterious by PolyPhen and SIFT in silico analyses, respectively. Since supporting evidence is limited at this time, the clinical significance of p.I159M remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Feb 28, 2024