NC_000016.10:g.67660378C>G AND Dyskeratosis congenita, autosomal dominant 6

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 1, 2023
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:: RCV003755375.2

Allele description [Variation Report for NC_000016.10:g.67660378C>G]

NC_000016.10:g.67660378C>G

Genes:

ACD:ACD shelterin complex subunit and telomerase recruitment factor [Gene - OMIM - HGNC]
LOC130059224:ATAC-STARR-seq lymphoblastoid silent region 7617 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NC_000016.10:g.67660378C>G

HGVS:

NC_000016.10:g.67660378C>G
NG_042874.1:g.5438G>C
NG_193645.1:g.152C>G
NM_001082486.1:c.101G>C
NM_022914.2:c.101G>C
NP_001075955.1:p.Arg34Pro
NP_075065.2:p.Arg34Pro
LRG_1237:g.5438G>C
NC_000016.9:g.67694281C>G

Protein change:

R34P

Molecular consequence:

NM_001082486.1:c.101G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_022914.2:c.101G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Dyskeratosis congenita, autosomal dominant 6 (DKCA6)
Identifiers:: MONDO: MONDO:0014690; MedGen: C4225284; Orphanet: 3322; OMIM: 616553

Recent activity

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SIGNAL PEPTIDE PEPTIDASE-LIKE 4 [Arabidopsis thaliana]
SIGNAL PEPTIDE PEPTIDASE-LIKE 4 [Arabidopsis thaliana]
gi|79333554|ref|NP_171671.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004405051	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 1, 2023)	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

SCV004405051

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 1, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV004405051.1

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The proline amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with ACD-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with proline, which is neutral and non-polar, at codon 34 of the ACD protein (p.Arg34Pro).

#	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: Nov 10, 2024

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