NM_001363.4(DKC1):c.1461C>T (p.Ala487=) AND not specified

Clinical significance:Conflicting interpretations of pathogenicity, Benign(2);Likely benign(1) (Last evaluated: May 6, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000116876.4

Allele description [Variation Report for NM_001363.4(DKC1):c.1461C>T (p.Ala487=)]

NM_001363.4(DKC1):c.1461C>T (p.Ala487=)

Gene:
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001363.4(DKC1):c.1461C>T (p.Ala487=)
HGVS:
  • NC_000023.11:g.154776309C>T
  • NG_009780.1:g.18554C>T
  • NM_001288747.1:c.*687C>T
  • NM_001363.4:c.1461C>T
  • NP_001354.1:p.Ala487=
  • LRG_55:g.18554C>T
  • LRG_55p1:p.Ala487=
  • NC_000023.10:g.154004584C>T
  • NM_001363.3:c.1461C>T
  • NR_110021.1:n.2162C>T
Links:
dbSNP: 1127051
GMAF:
0.0617(T), 1127051
NCBI 1000 Genomes Browser:
rs1127051
Allele Frequency:
NaN, GO-ESP
Molecular consequence:
  • NM_001288747.1:c.*687C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NR_110021.1:n.2162C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001363.4:c.1461C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
10

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000150961Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000226074EGL Genetic Diagnostics,Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(May 6, 2015)
germlineclinical testing

Citation Link,

SCV000307655PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown10not providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150961.2

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

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From EGL Genetic Diagnostics,Eurofins Clinical Diagnostics, SCV000226074.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided10not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided10not providednot providednot provided

From PreventionGenetics, SCV000307655.1

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

Last Updated: Sep 27, 2017