NM_000051.4(ATM):c.7674TAT[1] (p.Ile2560del) AND Ataxia-telangiectasia syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 27, 2021
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:: RCV001862379.14

Allele description [Variation Report for NM_000051.4(ATM):c.7674TAT[1] (p.Ile2560del)]

NM_000051.4(ATM):c.7674TAT[1] (p.Ile2560del)

Genes:

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

Variant type:

Microsatellite

Cytogenetic location:

11q22.3

Genomic location:

Preferred name:

NM_000051.4(ATM):c.7674TAT[1] (p.Ile2560del)

HGVS:

NC_000011.10:g.108331923TAT[1]
NC_000011.10:g.108331923_108331925TAT[1]
NG_009830.1:g.114092TAT[1]
NG_054724.1:g.142906TAA[1]
NM_000051.4:c.7674TAT[1]MANE SELECT
NM_001330368.2:c.641-22853_641-22851del
NM_001351110.2:c.*38+3296_*38+3298del
NM_001351834.2:c.7674TAT[1]
NP_000042.3:p.Ile2560del
NP_000042.3:p.Ile2560del
NP_001338763.1:p.Ile2560del
LRG_135t1:c.7674_7676TAT[1]
LRG_135:g.114092TAT[1]
LRG_135p1:p.Ile2560del
NC_000011.9:g.108202649_108202651del
NC_000011.9:g.108202650TAT[1]
NM_000051.3:c.7674_7676TAT[1]
NM_000051.3:c.7677_7679delTAT

Protein change:

I2560del

Links:

dbSNP: rs1591171617

NCBI 1000 Genomes Browser:

rs1591171617

Molecular consequence:

NM_000051.4:c.7674TAT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001351834.2:c.7674TAT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001330368.2:c.641-22853_641-22851del - intron variant - [Sequence Ontology: SO:0001627]
NM_001351110.2:c.*38+3296_*38+3298del - intron variant - [Sequence Ontology: SO:0001627]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002266543	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 27, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002266543

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 27, 2021)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002266543.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 827188). This variant has not been reported in the literature in individuals affected with ATM-related conditions. This variant is not present in population databases (ExAC no frequency). This variant, c.7677_7679del, results in the deletion of 1 amino acid(s) of the ATM protein (p.Ile2560del), but otherwise preserves the integrity of the reading frame.

#	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 17, 2024

ClinVar

Relating variation to medicine