NM_001184.4(ATR):c.1127G>T (p.Cys376Phe) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 15, 2023
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:: RCV003103028.3

Allele description [Variation Report for NM_001184.4(ATR):c.1127G>T (p.Cys376Phe)]

NM_001184.4(ATR):c.1127G>T (p.Cys376Phe)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3q23

Genomic location:

Preferred name:

NM_001184.4(ATR):c.1127G>T (p.Cys376Phe)

HGVS:

NC_000003.12:g.142562275C>A
NG_008951.1:g.21552G>T
NM_001184.4:c.1127G>TMANE SELECT
NM_001354579.2:c.1127G>T
NP_001175.2:p.Cys376Phe
NP_001341508.1:p.Cys376Phe
LRG_1403t1:c.1127G>T
LRG_1403:g.21552G>T
LRG_1403p1:p.Cys376Phe
NC_000003.11:g.142281117C>A
NM_001184.3:c.1127G>T

Protein change:

C376F

Molecular consequence:

NM_001184.4:c.1127G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354579.2:c.1127G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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isy1 ISY1 splicing factor homolog [Danio rerio]
isy1 ISY1 splicing factor homolog [Danio rerio]
Gene ID:570205

Gene
Homo sapiens golgin A4 (GOLGA4), transcript variant 7, mRNA
Homo sapiens golgin A4 (GOLGA4), transcript variant 7, mRNA
gi|2716983420|ref|NM_001429196.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003253296	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 15, 2023)	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

SCV003253296

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 15, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003253296.2

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1799438). This variant has not been reported in the literature in individuals affected with ATR-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 376 of the ATR protein (p.Cys376Phe).

#	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 29, 2024

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