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NM_005432.4(XRCC3):c.925G>A (p.Gly309Ser) AND not provided

Germline classification:
Uncertain significance (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001357230.1

Allele description [Variation Report for NM_005432.4(XRCC3):c.925G>A (p.Gly309Ser)]

NM_005432.4(XRCC3):c.925G>A (p.Gly309Ser)

Genes:
XRCC3:X-ray repair cross complementing 3 [Gene - OMIM - HGNC]
KLC1:kinesin light chain 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q32.33
Genomic location:
Preferred name:
NM_005432.4(XRCC3):c.925G>A (p.Gly309Ser)
HGVS:
  • NC_000014.9:g.103698914C>T
  • NG_011516.1:g.21573G>A
  • NG_012307.1:g.74727C>T
  • NM_001100118.2:c.925G>A
  • NM_001100119.2:c.925G>A
  • NM_001130107.2:c.1782-1741C>T
  • NM_001371229.1:c.925G>A
  • NM_001371231.1:c.925G>A
  • NM_001371232.1:c.925G>A
  • NM_001394832.1:c.1924-1741C>T
  • NM_001394834.1:c.1897-1741C>T
  • NM_001394836.1:c.1857-1741C>T
  • NM_001394837.1:c.1849-1741C>TMANE SELECT
  • NM_001394839.1:c.1830-1741C>T
  • NM_001394840.1:c.1822-1741C>T
  • NM_001394842.1:c.1779-1741C>T
  • NM_001394843.1:c.1776-1741C>T
  • NM_001394844.1:c.1755-1741C>T
  • NM_001394846.1:c.1726-1741C>T
  • NM_001394848.1:c.1699-1741C>T
  • NM_001394851.1:c.1645-1741C>T
  • NM_001394852.1:c.1624-1741C>T
  • NM_005432.4:c.925G>AMANE SELECT
  • NM_182923.4:c.1651-1741C>T
  • NP_001093588.1:p.Gly309Ser
  • NP_001093589.1:p.Gly309Ser
  • NP_001358158.1:p.Gly309Ser
  • NP_001358160.1:p.Gly309Ser
  • NP_001358161.1:p.Gly309Ser
  • NP_005423.1:p.Gly309Ser
  • NC_000014.8:g.104165251C>T
  • NM_001100119.1:c.925G>A
Protein change:
G309S
Links:
dbSNP: rs532124840
NCBI 1000 Genomes Browser:
rs532124840
Molecular consequence:
  • NM_001130107.2:c.1782-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394832.1:c.1924-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394834.1:c.1897-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394836.1:c.1857-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394837.1:c.1849-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394839.1:c.1830-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394840.1:c.1822-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394842.1:c.1779-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394843.1:c.1776-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394844.1:c.1755-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394846.1:c.1726-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394848.1:c.1699-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394851.1:c.1645-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001394852.1:c.1624-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_182923.4:c.1651-1741C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001100118.2:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001100119.2:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371229.1:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371231.1:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001371232.1:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005432.4:c.925G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001552632Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided
Uncertain significanceunknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001552632.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The XRCC3 p.Gly309Ser variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs532124840) and in control databases in 65 of 253456 chromosomes at a frequency of 0.0002565 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: South Asian in 59 of 28102 chromosomes (freq: 0.002099), East Asian in 3 of 18218 chromosomes (freq: 0.000165), Other in 1 of 6638 chromosomes (freq: 0.000151) and European (non-Finnish) in 2 of 113534 chromosomes (freq: 0.000018), but was not observed in the African, Latino, Ashkenazi Jewish, or European (Finnish) populations. The p.Gly309 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 2 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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

Last Updated: Sep 1, 2024