NM_000314.8(PTEN):c.321T>C (p.Asp107=) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: Oct 8, 2019)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000590378.5

Allele description [Variation Report for NM_000314.8(PTEN):c.321T>C (p.Asp107=)]

NM_000314.8(PTEN):c.321T>C (p.Asp107=)

Gene:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.8(PTEN):c.321T>C (p.Asp107=)
HGVS:
  • NC_000010.11:g.87933080T>C
  • NG_007466.2:g.74642T>C
  • NM_000314.8:c.321T>CMANE SELECT
  • NM_001304717.5:c.840T>C
  • NM_001304718.2:c.-430T>C
  • NP_000305.3:p.Asp107=
  • NP_001291646.4:p.Asp280=
  • LRG_311t1:c.321T>C
  • LRG_311:g.74642T>C
  • NC_000010.10:g.89692837T>C
  • NM_000314.4:c.321T>C
  • NM_000314.6:c.321T>C
  • p.D107D
Links:
dbSNP: rs372876243
NCBI 1000 Genomes Browser:
rs372876243
Molecular consequence:
  • NM_001304718.2:c.-430T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000314.8:c.321T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001304717.5:c.840T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000514310GeneDxcriteria provided, single submitter
Likely benign
(Sep 16, 2019)
germlineclinical testing

Citation Link,

SCV000696533Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Jan 10, 2017)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001469638Quest Diagnostics Nichols Institute San Juan Capistranocriteria provided, single submitter
Likely benign
(Oct 8, 2019)
unknownclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]
PMID:
26467025
PMCID:
PMC4737317

Details of each submission

From GeneDx, SCV000514310.5

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696533.1

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

Description

Variant summary: The PTEN c.321T>C (p.Asp107Asp) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 3/121362 control chromosomes at a frequency of 0.0000247, which is approximately 4 times the estimated maximal expected allele frequency of a pathogenic PTEN variant (0.0000063), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. One LCA sample also carried pathogenic variants in BRCA2 c.1796_1800delCTTAT/p.S599X and c.4092_4093insAA/p.C1365fsX10, further supporting the benign classification of this variant. Taken together, this variant is classified as benign.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001469638.1

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

Last Updated: Dec 4, 2021

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