NM_005732.4(RAD50):c.416A>G (p.Glu139Gly) AND Hereditary cancer-predisposing syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 2, 2020
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:: RCV001349075.6

Allele description

NM_005732.4(RAD50):c.416A>G (p.Glu139Gly)

Gene:

RAD50:RAD50 double strand break repair protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q31.1

Genomic location:

Preferred name:

NM_005732.4(RAD50):c.416A>G (p.Glu139Gly)

HGVS:

NC_000005.10:g.132579367A>G
NG_021151.2:g.27391A>G
NM_005732.4:c.416A>GMANE SELECT
NP_005723.2:p.Glu139Gly
LRG_312t1:c.416A>G
LRG_312:g.27391A>G
LRG_312p1:p.Glu139Gly
NC_000005.9:g.131915059A>G

Protein change:

E139G

Links:

dbSNP: rs1750461273

NCBI 1000 Genomes Browser:

rs1750461273

Molecular consequence:

NM_005732.4:c.416A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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uncharacterized protein C15orf39 isoform X1 [Homo sapiens]
uncharacterized protein C15orf39 isoform X1 [Homo sapiens]
gi|2217302086|ref|XP_047288820.1|

Protein
Homo sapiens Ras association and DIL domains, mRNA (cDNA clone MGC:150926 IMAGE:...
Homo sapiens Ras association and DIL domains, mRNA (cDNA clone MGC:150926 IMAGE:40125868), complete cds
gi|111599558|gb|BC117317.1|

Nucleotide
Homo sapiens CD207 molecule, langerin, mRNA (cDNA clone MGC:22374 IMAGE:4692155)...
Homo sapiens CD207 molecule, langerin, mRNA (cDNA clone MGC:22374 IMAGE:4692155), complete cds
gi|18490603|gb|BC022278.1|

Nucleotide
MULTISPECIES: 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygen...
MULTISPECIES: 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase reductase subunit [Amycolatopsis]
gi|740730740|ref|WP_038516026.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001543402	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 2, 2020)	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

SCV001543402

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 2, 2020)

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, SCV001543402.4

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with RAD50-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with glycine at codon 139 of the RAD50 protein (p.Glu139Gly). The glutamic acid residue is moderately conserved and there is a moderate physicochemical difference between glutamic acid and glycine.

#	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: Mar 5, 2024

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