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NM_001363.4(DKC1):c.-142C>G AND Dyskeratosis congenita

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Jan 24, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001442049.13

Allele description

NM_001363.4(DKC1):c.-142C>G

Genes:
DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]
LOC130068886:ATAC-STARR-seq lymphoblastoid silent region 21118 [Gene]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_001363.4(DKC1):c.-142C>G
HGVS:
  • NC_000023.11:g.154762824C>G
  • NG_009780.1:g.5069C>G
  • NG_203300.1:g.280C>G
  • NM_001142463.2:c.-142C>G
  • NM_001288747.1:c.-142C>G
  • NM_001363.4:c.-142C>G
  • LRG_55t1:c.-142C>G
  • LRG_55:g.5069C>G
  • NC_000023.10:g.153991099C>G
  • NM_001288747.1:c.-142C>G
  • NM_001363.3:c.-142C>G
  • NM_001363.5:c.-142C>GMANE SELECT
  • NR_110021.1:n.83C>G
  • NR_110022.1:n.83C>G
  • NR_110023.1:n.83C>G
Nucleotide change:
-141C-G, PROMOTER
Links:
OMIM: 300126.0008; dbSNP: rs199422241
NCBI 1000 Genomes Browser:
rs199422241

Condition(s)

Name:
Dyskeratosis congenita
Identifiers:
MONDO: MONDO:0015780; MedGen: C0265965; OMIM: PS127550

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001644990Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Jan 24, 2024) 		germlineclinical testing

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

SCV002535823Sema4, Sema4
criteria provided, single submitter

(Sema4 Curation Guidelines)		Benign
(Dec 17, 2020) 		germlinecuration

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001644990.3

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

From Sema4, Sema4, SCV002535823.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 20, 2024