NM_001363.5(DKC1):c.1156G>A (p.Ala386Thr) AND Dyskeratosis congenita, X-linked

Germline classification:: Pathogenic (3 submissions)
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:: RCV000032187.6

Allele description [Variation Report for NM_001363.5(DKC1):c.1156G>A (p.Ala386Thr)]

NM_001363.5(DKC1):c.1156G>A (p.Ala386Thr)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

Xq28

Genomic location:

Preferred name:

NM_001363.5(DKC1):c.1156G>A (p.Ala386Thr)

HGVS:

NC_000023.11:g.154774602G>A
NG_009780.1:g.16847G>A
NM_001142463.3:c.1156G>A
NM_001288747.2:c.1156G>A
NM_001363.5:c.1156G>AMANE SELECT
NP_001135935.1:p.Ala386Thr
NP_001275676.1:p.Ala386Thr
NP_001354.1:p.Ala386Thr
LRG_55t1:c.1156G>A
LRG_55:g.16847G>A
NC_000023.10:g.154002877G>A
NM_001363.3:c.1156G>A
NM_001363.5:c.1156G>A
NR_110021.2:n.1735G>A
NR_110022.2:n.1854G>A
NR_110023.2:n.1628G>A

Protein change:

A386T

Links:

dbSNP: rs199422252

NCBI 1000 Genomes Browser:

rs199422252

Molecular consequence:

NM_001142463.3:c.1156G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001288747.2:c.1156G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363.5:c.1156G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_110021.2:n.1735G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110022.2:n.1854G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_110023.2:n.1628G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Dyskeratosis congenita, X-linked (DKCX)
Synonyms:: Zinsser-Cole-Engman Syndrome
Identifiers:: MONDO: MONDO:0010584; MedGen: C1148551; OMIM: 305000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000055775	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (1) [See all records that cite this PMID]
SCV002053757	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	maternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002097631	Institutes of Biomedical Sciences, Shanxi University	no assertion criteria provided	Benign	inherited	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000055775

GeneReviews

no classification provided

not provided

unknown

literature only

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

SCV002053757

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

maternal

clinical testing

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

SCV002097631

Institutes of Biomedical Sciences, Shanxi University

no assertion criteria provided

Benign

inherited

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	maternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Dyskeratosis Congenita and Related Telomere Biology Disorders.

Savage SA, Niewisch MR.

2009 Nov 12 [updated 2023 Jan 19]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 20301779

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 GeneReviews, SCV000055775.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	not provided	not provided	not provided	Assert pathogenicity		not provided	not provided	not provided	not provided

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053757.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	maternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institutes of Biomedical Sciences, Shanxi University, SCV002097631.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Feb 25, 2023

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