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NM_000051.4(ATM):c.7875_7876delinsGC (p.Asp2625_Ala2626delinsGluPro) AND Ataxia-telangiectasia syndrome

Germline classification:
Pathogenic/Likely pathogenic (6 submissions)
Last evaluated:
Jan 29, 2024
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:
RCV000202436.23

Allele description [Variation Report for NM_000051.4(ATM):c.7875_7876delinsGC (p.Asp2625_Ala2626delinsGluPro)]

NM_000051.4(ATM):c.7875_7876delinsGC (p.Asp2625_Ala2626delinsGluPro)

Genes:
ATM:ATM serine/threonine kinase [Gene - OMIM - HGNC]
C11orf65:chromosome 11 open reading frame 65 [Gene - HGNC]
Variant type:
Indel
Cytogenetic location:
11q22.3
Genomic location:
Preferred name:
NM_000051.4(ATM):c.7875_7876delinsGC (p.Asp2625_Ala2626delinsGluPro)
Other names:
LRG_135t1:c.7875_7876delTGinsGC
HGVS:
  • NC_000011.10:g.108332848_108332849delinsGC
  • NG_009830.1:g.115017_115018delTGinsGC
  • NG_009830.1:g.115017_115018delinsGC
  • NG_054724.1:g.141984_141985delinsGC
  • NM_000051.4:c.7875_7876delinsGCMANE SELECT
  • NM_001330368.2:c.641-23778_641-23777delinsGC
  • NM_001351110.2:c.*38+2371_*38+2372delinsGC
  • NM_001351834.2:c.7875_7876delinsGC
  • NP_000042.3:p.Asp2625_Ala2626delinsGluPro
  • NP_000042.3:p.Asp2625_Ala2626delinsGluPro
  • NP_001338763.1:p.Asp2625_Ala2626delinsGluPro
  • LRG_135t1:c.7875_7876delinsGC
  • LRG_135:g.115017_115018delTGinsGC
  • LRG_135:g.115017_115018delinsGC
  • NC_000011.10:g.108332848_108332849delTGinsGC
  • NC_000011.9:g.108203575_108203576delinsGC
  • NG_009830.1:g.115017_115018delTGinsGC
  • NM_000051.3:c.7875_7876delTGinsGC
  • NM_000051.3:c.7875_7876delTGinsGC
  • NM_000051.3:c.7875_7876delinsGC
Protein change:
ASP2625GLU, ALA2626PRO
Links:
OMIM: 607585.0013; dbSNP: rs267606668
NCBI 1000 Genomes Browser:
rs267606668
Molecular consequence:
  • NM_001330368.2:c.641-23778_641-23777delinsGC - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001351110.2:c.*38+2371_*38+2372delinsGC - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000051.4:c.7875_7876delinsGC - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001351834.2:c.7875_7876delinsGC - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ataxia-telangiectasia syndrome (AT)
Synonyms:
Louis-Bar syndrome; Cerebello-oculocutaneous telangiectasia; Immunodeficiency with ataxia telangiectasia; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008840; MedGen: C0004135; Orphanet: 100; OMIM: 208900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000023327OMIM
no assertion criteria provided
Pathogenic
(Apr 30, 2004)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV000189490ClinVar Staff, National Center for Biotechnology Information (NCBI)
no classification provided
not providednot providednot provided

SCV000486124Counsyl
criteria provided, single submitter

(Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))
Likely pathogenic
(Apr 6, 2016)
unknownclinical testing

PubMed (9)
[See all records that cite these PMIDs]

mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf,

Citation Link,

SCV000546759Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 29, 2024)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV000838600Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Pathogenic
(Jul 2, 2018)
unknownclinical testing

Citation Link,

SCV003929076Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Apr 10, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Prediction of the secondary structure of proteins from their amino acid sequence.

Chou PY, Fasman GD.

Adv Enzymol Relat Areas Mol Biol. 1978;47:45-148. Review. No abstract available.

PubMed [citation]
PMID:
364941

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins.

Garnier J, Osguthorpe DJ, Robson B.

J Mol Biol. 1978 Mar 25;120(1):97-120. No abstract available.

PubMed [citation]
PMID:
642007
See all PubMed Citations (13)

Details of each submission

From OMIM, SCV000023327.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In a Dutch family, van Belzen et al. (1998) demonstrated that affected members with ataxia-telangiectasia (AT; 208900) were homozygous for 2 consecutive base substitutions in exon 55 of the ATM gene: a T-to-G transversion at position 7875 of the ATM cDNA and a G-to-C transversion at position 7876. The double base substitution resulted in an amino acid change of an aspartic acid to a glutamic acid at codon 2625 (D2625E) and of an alanine to a proline at codon 2626 (A2626P) of the ATM protein. Both amino acids are conserved between the ATM protein and its functional homolog, the Atm gene product in the mouse. The change in secondary structure of the ATM protein carrying the D2625E/A2626P mutation, as predicted by the method of Chou and Fasman (1978) and of Garnier et al. (1978), suggested that the double base substitution is a disease-causing mutation.

Dork et al. (2004) described a patient with an attenuated form of AT in whom the disorder was diagnosed at the age of 52 years and who died at the age of 60 years. He was found to be a compound heterozygote for a double missense mutation (D2625E and A2626P) and a novel splicing mutation (496+5G-A; 607585.0031) of the ATM gene. Cytogenetic studies of the patient's lymphoblastoid cells revealed modest levels of bleomycin-induced chromosomal instability. Residual ATM protein was 10 to 20% of wildtype. Low residual ATM kinase activity could be demonstrated towards p53 (191170), whereas it was poorly detectable towards nibrin (602667). The results corroborated the view that the clinical variability of AT is partly determined by the mutation type and indicated that AT can present as a late adulthood disease. Although ataxia-telangiectasia was diagnosed at the age of 52 years, the patient had developed the first symptoms of ataxia at the age of 7 years. Ataxia had become prominent by the age of 14 years, and he had lost the ability to walk alone by the age of 22 years. He became permanently wheelchair-bound by the age of 45 years. Clinical diagnosis was made at the age of 52 years and confirmed by cytogenetic analysis 3 years later. His clinical phenotype thereafter was progressively dominated by chronic obstipation associated with megacolon and gastroenteritis.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From ClinVar Staff, National Center for Biotechnology Information (NCBI), SCV000189490.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From Counsyl, SCV000486124.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000546759.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This variant, c.7875_7876delinsGC, is a complex sequence change that results in the substitution of 2 amino acid(s) in the ATM protein (p.Asp2625_Ala2626delinsGluPro). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This variant has been observed in individual(s) with ataxia telangiectasia (PMID: 9521587, 10980530, 19535770, 22213089). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as a double missense variant, D2625E and A2626P on the same chromosome. ClinVar contains an entry for this variant (Variation ID: 3030). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects ATM function (PMID: 22213089). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Mendelics, SCV000838600.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003929076.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: ATM c.7875_7876delinsGC (p.Asp2625_Ala2626delinsGluPro) results in an in-frame deletion-insertion that is predicted to delete two amino acids and insert to amino acids from the encoded protein. The variant was absent in 250852 control chromosomes (gnomAD). c.7875_7876delinsGC has been reported in the literature in multiple bi-allelic individuals affected with Ataxia-Telangiectasia (example: Verhagen_2012). These data indicate that the variant is very likely to be associated with disease. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024