NM_000051.4(ATM):c.5712dup (p.Ser1905fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 7, 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:: RCV000212031.29

Allele description [Variation Report for NM_000051.4(ATM):c.5712dup (p.Ser1905fs)]

NM_000051.4(ATM):c.5712dup (p.Ser1905fs)

Gene:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.5712dup (p.Ser1905fs)

HGVS:

NC_000011.10:g.108307934dup
NG_009830.1:g.90103dup
NG_054724.1:g.166904dup
NM_000051.4:c.5712dupMANE SELECT
NM_001351834.2:c.5712dup
NP_000042.3:p.Ser1905fs
NP_000042.3:p.Ser1905fs
NP_001338763.1:p.Ser1905fs
LRG_135t1:c.5712dup
LRG_135:g.90103dup
LRG_135p1:p.Ser1905fs
NC_000011.9:g.108178655_108178656insA
NC_000011.9:g.108178661dup
NM_000051.3:c.5712dup
NM_000051.3:c.5712dupA
NM_000051.4:c.5712dupAMANE SELECT
p.S1905Ifs*25
p.S1905IfsX25

Protein change:

S1905fs

Links:

dbSNP: rs587781730

NCBI 1000 Genomes Browser:

rs587781730

Molecular consequence:

NM_000051.4:c.5712dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.5712dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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CD59 glycoprotein preproprotein [Homo sapiens]
CD59 glycoprotein preproprotein [Homo sapiens]
gi|187828910|ref|NP_001120695.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000209623	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 7, 2022)	germline	clinical testing	Citation Link,
SCV001961309	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Sep 1, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000209623

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 7, 2022)

germline

clinical testing

Citation Link,

SCV001961309

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Pathogenic
(Sep 1, 2021)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000209623.14

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

Description

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Observed in the heterozygous state in individuals with a personal and/or family history of ATM-related cancers (Tung et al., 2015; Antonarakis et al., 2018; Lowery et al., 2018; Girard et al., 2019); This variant is associated with the following publications: (PMID: 10873394, 8845835, 10817650, 26681312, 26270727, 25186627, 7792600, 16266405, 24763289, 18321536, 29506128, 30303537, 26689913, 31447099, 28843361, 29439820, 32754152, 33547824, 32866655, 34992599, 35365198, 32782288, 33804961, 29922827, 25614872, 23807571, 35366121, 35448200, 31050087)

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

From CeGaT Center for Human Genetics Tuebingen, SCV001961309.20

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

Last Updated: Oct 20, 2024

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