NM_001363.5(DKC1):c.42GAA[1] (p.Lys17del) AND Dyskeratosis congenita

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 14, 2022
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:: RCV001233988.5

Allele description [Variation Report for NM_001363.5(DKC1):c.42GAA[1] (p.Lys17del)]

NM_001363.5(DKC1):c.42GAA[1] (p.Lys17del)

Gene:

DKC1:dyskerin pseudouridine synthase 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001363.5(DKC1):c.42GAA[1] (p.Lys17del)

HGVS:

NC_000023.11:g.154764924GAA[1]
NG_009780.1:g.7169GAA[1]
NM_001142463.3:c.42GAA[1]
NM_001288747.2:c.42GAA[1]
NM_001363.5:c.42GAA[1]MANE SELECT
NP_001135935.1:p.Lys17del
NP_001275676.1:p.Lys17del
NP_001354.1:p.Lys17del
LRG_55:g.7169GAA[1]
NC_000023.10:g.153993197_153993199del
NC_000023.10:g.153993199GAA[1]
NM_001363.4:c.45_47del
NM_001363.5:c.45_47delMANE SELECT
NR_110021.2:n.144GAA[1]
NR_110022.2:n.144GAA[1]
NR_110023.2:n.144GAA[1]

Protein change:

K17del

Links:

dbSNP: rs782201995

NCBI 1000 Genomes Browser:

rs782201995

Molecular consequence:

NM_001142463.3:c.42GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001288747.2:c.42GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001363.5:c.42GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_110021.2:n.144GAA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110022.2:n.144GAA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110023.2:n.144GAA[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001406611	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 14, 2022)	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

SCV001406611

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 14, 2022)

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, SCV001406611.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant, c.45_47del, results in the deletion of 1 amino acid(s) of the DKC1 protein (p.Lys17del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs782201995, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with DKC1-related conditions. ClinVar contains an entry for this variant (Variation ID: 960459). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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: Feb 7, 2023

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