NM_000051.4(ATM):c.4258C>T (p.Leu1420Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Jan 5, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000130979.23

Allele description [Variation Report for NM_000051.4(ATM):c.4258C>T (p.Leu1420Phe)]

NM_000051.4(ATM):c.4258C>T (p.Leu1420Phe)

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.4258C>T (p.Leu1420Phe)

Other names:

p.L1420F:CTT>TTT; NP_000042.3:p.Leu1420Phe

HGVS:

NC_000011.10:g.108289623C>T
NG_009830.1:g.71792C>T
NM_000051.4:c.4258C>TMANE SELECT
NM_001351834.2:c.4258C>T
NP_000042.3:p.Leu1420Phe
NP_000042.3:p.Leu1420Phe
NP_001338763.1:p.Leu1420Phe
LRG_135t1:c.4258C>T
LRG_135:g.71792C>T
LRG_135p1:p.Leu1420Phe
NC_000011.9:g.108160350C>T
NM_000051.3:c.4258C>T
Q13315:p.Leu1420Phe
p.L1420F

Protein change:

L1420F

Links:

UniProtKB: Q13315#VAR_010822; dbSNP: rs1800058

NCBI 1000 Genomes Browser:

rs1800058

Molecular consequence:

NM_000051.4:c.4258C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.4258C>T - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000185896	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Jan 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 17132159, 27153395 Citation Link,
SCV000266991	Vantari Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Feb 3, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000537361	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Nov 24, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000787864	True Health Diagnostics	no assertion criteria provided	Benign (Feb 20, 2018)	germline	clinical testing
SCV000803143	Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (May 23, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Comprehensive analysis of the ATM, CHEK2 and ERBB2 genes in relation to breast tumour characteristics and survival: a population-based case-control and follow-up study.

Einarsdóttir K, Rosenberg LU, Humphreys K, Bonnard C, Palmgren J, Li Y, Li Y, Chia KS, Liu ET, Hall P, Liu J, Wedrén S.

Breast Cancer Res. 2006;8(6):R67.

PubMed [citation]

PMID:: 17132159
PMCID:: PMC1797028

Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer.

Maxwell KN, Hart SN, Vijai J, Schrader KA, Slavin TP, Thomas T, Wubbenhorst B, Ravichandran V, Moore RM, Hu C, Guidugli L, Wenz B, Domchek SM, Robson ME, Szabo C, Neuhausen SL, Weitzel JN, Offit K, Couch FJ, Nathanson KL.

Am J Hum Genet. 2016 May 5;98(5):801-817. doi: 10.1016/j.ajhg.2016.02.024.

PubMed [citation]

PMID:: 27153395
PMCID:: PMC4863474

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000185896.6

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Vantari Genetics, SCV000266991.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV000537361.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From True Health Diagnostics, SCV000787864.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C., SCV000803143.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 29, 2024

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