NM_000051.4(ATM):c.7865C>T (p.Ala2622Val) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: May 1, 2023
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:: RCV000521492.20

Allele description [Variation Report for NM_000051.4(ATM):c.7865C>T (p.Ala2622Val)]

NM_000051.4(ATM):c.7865C>T (p.Ala2622Val)

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.7865C>T (p.Ala2622Val)

HGVS:

NC_000011.10:g.108332838C>T
NG_009830.1:g.115007C>T
NG_054724.1:g.141995G>A
NM_000051.4:c.7865C>TMANE SELECT
NM_001330368.2:c.641-23767G>A
NM_001351110.2:c.*38+2382G>A
NM_001351834.2:c.7865C>T
NP_000042.3:p.Ala2622Val
NP_000042.3:p.Ala2622Val
NP_001338763.1:p.Ala2622Val
LRG_135t1:c.7865C>T
LRG_135:g.115007C>T
LRG_135p1:p.Ala2622Val
NC_000011.9:g.108203565C>T
NM_000051.3:c.7865C>T

Protein change:

A2622V

Links:

dbSNP: rs766351395

NCBI 1000 Genomes Browser:

rs766351395

Molecular consequence:

NM_001330368.2:c.641-23767G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+2382G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000051.4:c.7865C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001351834.2:c.7865C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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unnamed protein product [Rattus sp.]
unnamed protein product [Rattus sp.]
gi|57786|emb|CAA34497.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000617375	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 23, 2022)	germline	clinical testing	Citation Link,
SCV004010116	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely pathogenic (May 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000617375

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Nov 23, 2022)

germline

clinical testing

Citation Link,

SCV004010116

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Likely pathogenic
(May 1, 2023)

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, SCV000617375.3

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

Description

Missense variant that results in aberrant splicing and a null allele in a gene for which loss of function is a known mechanism of disease (Bullrich et al., 1999; Teraoka et al., 1999; Du et al., 2007); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as c.8250C>T; Missense variant that results in aberrant splicing and a null allele in a gene for which loss of function is a known mechanism of disease (Bullrich et al., 1999; Teraoka et al., 1999; Du et al., 2007); This variant is associated with the following publications: (PMID: 24568663, 33624863, 20945614, 16411093, 10330348, 14695534, 24506781, 18321536, 21576124, 17389389, 9892178, 34426522, 32899500)

#	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, SCV004010116.12

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

Description

ATM: PM2, PS4:Moderate, PP3, PS3:Supporting

#	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: Nov 10, 2024

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