NM_000051.4(ATM):c.6369_6370del (p.Ser2123fs) AND Familial prostate cancer

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 6, 2024
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:: RCV004525975.2

Allele description [Variation Report for NM_000051.4(ATM):c.6369_6370del (p.Ser2123fs)]

NM_000051.4(ATM):c.6369_6370del (p.Ser2123fs)

Genes:

ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.6369_6370del (p.Ser2123fs)

HGVS:

NC_000011.10:g.108319975_108319976del
NG_009830.1:g.102144_102145del
NG_054724.1:g.154857_154858del
NM_000051.4:c.6369_6370delMANE SELECT
NM_001330368.2:c.641-10905_641-10904del
NM_001351110.2:c.*39-10905_*39-10904del
NM_001351834.2:c.6369_6370del
NP_000042.3:p.Ser2123Argfs
NP_000042.3:p.Ser2123fs
NP_001338763.1:p.Ser2123fs
LRG_135t1:c.6369_6370del
LRG_135:g.102144_102145del
LRG_135p1:p.Ser2123Argfs
NC_000011.9:g.108190702_108190703del
NM_000051.3:c.6369_6370delTT
NM_000051.3:c.6369_6370delTT
NM_000051.4:c.6369_6370delTTMANE SELECT

Protein change:

S2123fs

Links:

dbSNP: rs1555116381

NCBI 1000 Genomes Browser:

rs1555116381

Molecular consequence:

NM_000051.4:c.6369_6370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001351834.2:c.6369_6370del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330368.2:c.641-10905_641-10904del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*39-10905_*39-10904del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Familial prostate cancer
Synonyms:: Hereditary prostate cancer
Identifiers:: MONDO: MONDO:0700275; MedGen: C2931456; OMIM: 176807

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AWPM-19-like family protein [Arabidopsis thaliana]
AWPM-19-like family protein [Arabidopsis thaliana]
gi|15239619|ref|NP_197398.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005040130	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Mar 6, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005040130

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Mar 6, 2024)

germline

clinical testing

Citation Link

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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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV005040130.2

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

Description

Variant summary: ATM c.6369_6370delTT (p.Ser2123ArgfsX3) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 249538 control chromosomes. To our knowledge, no occurrence of c.6369_6370delTT in individuals affected with Prostate Cancer and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 479029). Based on the evidence outlined above, the variant was classified as pathogenic.

#	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: Sep 16, 2024

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