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NC_000016.9:g.(?_65821800)_(72146396_?)del AND Dyskeratosis congenita, autosomal dominant 6

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 23, 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:
RCV003122496.3

Allele description

NC_000016.9:g.(?_65821800)_(72146396_?)del

Genes:
  • ACD:ACD shelterin complex subunit and telomerase recruitment factor [Gene - OMIM - HGNC]
  • ATP6V0D1:ATPase H+ transporting V0 subunit d1 [Gene - OMIM - HGNC]
  • CLEC18A:C-type lectin domain family 18 member A [Gene - OMIM - HGNC]
  • CLEC18C:C-type lectin domain family 18 member C [Gene - OMIM - HGNC]
  • CTCF:CCCTC-binding factor [Gene - OMIM - HGNC]
  • CMTM1:CKLF like MARVEL transmembrane domain containing 1 [Gene - OMIM - HGNC]
  • CMTM2:CKLF like MARVEL transmembrane domain containing 2 [Gene - OMIM - HGNC]
  • CMTM3:CKLF like MARVEL transmembrane domain containing 3 [Gene - OMIM - HGNC]
  • CMTM4:CKLF like MARVEL transmembrane domain containing 4 [Gene - OMIM - HGNC]
  • CKLF-CMTM1:CKLF-CMTM1 readthrough [Gene - HGNC]
  • DDX19A:DEAD-box helicase 19A [Gene - HGNC]
  • DDX19B:DEAD-box helicase 19B [Gene - OMIM - HGNC]
  • DDX28:DEAD-box helicase 28 [Gene - OMIM - HGNC]
  • DHX38:DEAH-box helicase 38 [Gene - OMIM - HGNC]
  • E2F4:E2F transcription factor 4 [Gene - OMIM - HGNC]
  • FBXL8:F-box and leucine rich repeat protein 8 [Gene - OMIM - HGNC]
  • GFOD2:Gfo/Idh/MocA-like oxidoreductase domain containing 2 [Gene - OMIM - HGNC]
  • HYDIN:HYDIN axonemal central pair apparatus protein [Gene - OMIM - HGNC]
  • IST1:IST1 factor associated with ESCRT-III [Gene - OMIM - HGNC]
  • MARVELD3:MARVEL domain containing 3 [Gene - OMIM - HGNC]
  • MTSS2:MTSS I-BAR domain containing 2 [Gene - OMIM - HGNC]
  • NQO1:NAD(P)H quinone dehydrogenase 1 [Gene - OMIM - HGNC]
  • NAE1:NEDD8 activating enzyme E1 subunit 1 [Gene - OMIM - HGNC]
  • NOB1:NIN1 (RPN12) binding protein 1 homolog [Gene - OMIM - HGNC]
  • PHLPP2:PH domain and leucine rich repeat protein phosphatase 2 [Gene - OMIM - HGNC]
  • RANBP10:RAN binding protein 10 [Gene - OMIM - HGNC]
  • RIPOR1:RHO family interacting cell polarization regulator 1 [Gene - OMIM - HGNC]
  • RRAD:RRAD, Ras related glycolysis inhibitor and calcium channel regulator [Gene - OMIM - HGNC]
  • ST3GAL2:ST3 beta-galactoside alpha-2,3-sialyltransferase 2 [Gene - OMIM - HGNC]
  • THAP11:THAP domain containing 11 [Gene - OMIM - HGNC]
  • TRADD:TNFRSF1A associated via death domain [Gene - OMIM - HGNC]
  • B3GNT9:UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 9 [Gene - HGNC]
  • UTP4:UTP4 small subunit processome component [Gene - OMIM - HGNC]
  • VAC14:VAC14 component of PIKFYVE complex [Gene - OMIM - HGNC]
  • WWP2:WW domain containing E3 ubiquitin protein ligase 2 [Gene - OMIM - HGNC]
  • ZFP90:ZFP90 zinc finger protein [Gene - OMIM - HGNC]
  • AP1G1:adaptor related protein complex 1 subunit gamma 1 [Gene - OMIM - HGNC]
  • AGRP:agouti related neuropeptide [Gene - OMIM - HGNC]
  • AARS1:alanyl-tRNA synthetase 1 [Gene - OMIM - HGNC]
  • ATXN1L:ataxin 1 like [Gene - OMIM - HGNC]
  • BEAN1:brain expressed associated with NEDD4 1 [Gene - OMIM - HGNC]
  • CDH16:cadherin 16 [Gene - OMIM - HGNC]
  • CDH1:cadherin 1 [Gene - OMIM - HGNC]
  • CDH3:cadherin 3 [Gene - OMIM - HGNC]
  • CDH5:cadherin 5 [Gene - OMIM - HGNC]
  • CALB2:calbindin 2 [Gene - OMIM - HGNC]
  • CMTR2:cap methyltransferase 2 [Gene - OMIM - HGNC]
  • CARMIL2:capping protein regulator and myosin 1 linker 2 [Gene - OMIM - HGNC]
  • CHST4:carbohydrate sulfotransferase 4 [Gene - HGNC]
  • CA7:carbonic anhydrase 7 [Gene - OMIM - HGNC]
  • CES2:carboxylesterase 2 [Gene - OMIM - HGNC]
  • CES3:carboxylesterase 3 [Gene - OMIM - HGNC]
  • CES4A:carboxylesterase 4A [Gene - HGNC]
  • CENPT:centromere protein T [Gene - OMIM - HGNC]
  • CKLF:chemokine like factor [Gene - OMIM - HGNC]
  • C16orf86:chromosome 16 open reading frame 86 [Gene - HGNC]
  • CHTF8:chromosome transmission fidelity factor 8 [Gene - OMIM - HGNC]
  • CTRL:chymotrypsin like [Gene - OMIM - HGNC]
  • COG4:component of oligomeric golgi complex 4 [Gene - OMIM - HGNC]
  • COG8:component of oligomeric golgi complex 8 [Gene - OMIM - HGNC]
  • CBFB:core-binding factor subunit beta [Gene - OMIM - HGNC]
  • CYB5B:cytochrome b5 type B [Gene - OMIM - HGNC]
  • CIAO2B:cytosolic iron-sulfur assembly component 2B [Gene - OMIM - HGNC]
  • DHODH:dihydroorotate dehydrogenase (quinone) [Gene - OMIM - HGNC]
  • DUS2:dihydrouridine synthase 2 [Gene - OMIM - HGNC]
  • DPEP2:dipeptidase 2 [Gene - OMIM - HGNC]
  • DPEP3:dipeptidase 3 [Gene - OMIM - HGNC]
  • DYNC1LI2:dynein cytoplasmic 1 light intermediate chain 2 [Gene - OMIM - HGNC]
  • ELMO3:engulfment and cell motility 3 [Gene - OMIM - HGNC]
  • EDC4:enhancer of mRNA decapping 4 [Gene - OMIM - HGNC]
  • ENKD1:enkurin domain containing 1 [Gene - HGNC]
  • ESRP2:epithelial splicing regulatory protein 2 [Gene - OMIM - HGNC]
  • EXOC3L1:exocyst complex component 3 like 1 [Gene - OMIM - HGNC]
  • EXOSC6:exosome component 6 [Gene - OMIM - HGNC]
  • FHOD1:formin homology 2 domain containing 1 [Gene - OMIM - HGNC]
  • FCSK:fucose kinase [Gene - OMIM - HGNC]
  • HPR:haptoglobin-related protein [Gene - OMIM - HGNC]
  • HP:haptoglobin [Gene - OMIM - HGNC]
  • HSF4:heat shock transcription factor 4 [Gene - OMIM - HGNC]
  • HAS3:hyaluronan synthase 3 [Gene - OMIM - HGNC]
  • HSD11B2:hydroxysteroid 11-beta dehydrogenase 2 [Gene - OMIM - HGNC]
  • IL34:interleukin 34 [Gene - OMIM - HGNC]
  • LCAT:lecithin-cholesterol acyltransferase [Gene - OMIM - HGNC]
  • LRRC29:leucine rich repeat containing 29 [Gene - HGNC]
  • LRRC36:leucine rich repeat containing 36 [Gene - HGNC]
  • MIR140:microRNA 140 [Gene - OMIM - HGNC]
  • MIR328:microRNA 328 [Gene - OMIM - HGNC]
  • MATCAP1:microtubule associated tyrosine carboxypeptidase 1 [Gene - OMIM - HGNC]
  • NRN1L:neuritin 1 like [Gene - HGNC]
  • NFATC3:nuclear factor of activated T cells 3 [Gene - OMIM - HGNC]
  • NFAT5:nuclear factor of activated T cells 5 [Gene - OMIM - HGNC]
  • NUTF2:nuclear transport factor 2 [Gene - OMIM - HGNC]
  • NIP7:nucleolar pre-rRNA processing protein NIP7 [Gene - OMIM - HGNC]
  • NOL3:nucleolar protein 3 [Gene - OMIM - HGNC]
  • PARD6A:par-6 family cell polarity regulator alpha [Gene - OMIM - HGNC]
  • PDF:peptide deformylase, mitochondrial [Gene - OMIM - HGNC]
  • PHAF1:phagosome assembly factor 1 [Gene - HGNC]
  • PLA2G15:phospholipase A2 group XV [Gene - OMIM - HGNC]
  • PLEKHG4:pleckstrin homology and RhoGEF domain containing G4 [Gene - OMIM - HGNC]
  • PKD1L3:polycystin 1 like 3, transient receptor potential channel interacting [Gene - OMIM - HGNC]
  • KCTD19:potassium channel tetramerization domain containing 19 [Gene - OMIM - HGNC]
  • PSMB10:proteasome 20S subunit beta 10 [Gene - OMIM - HGNC]
  • PRMT7:protein arginine methyltransferase 7 [Gene - OMIM - HGNC]
  • PSKH1:protein serine kinase H1 [Gene - OMIM - HGNC]
  • PDP2:pyruvate dehydrogenase phosphatase catalytic subunit 2 [Gene - OMIM - HGNC]
  • PDPR:pyruvate dehydrogenase phosphatase regulatory subunit [Gene - OMIM - HGNC]
  • SLC12A4:solute carrier family 12 member 4 [Gene - OMIM - HGNC]
  • SLC7A6OS:solute carrier family 7 member 6 opposite strand [Gene - OMIM - HGNC]
  • SLC7A6:solute carrier family 7 member 6 [Gene - OMIM - HGNC]
  • SLC9A5:solute carrier family 9 member A5 [Gene - OMIM - HGNC]
  • SMPD3:sphingomyelin phosphodiesterase 3 [Gene - OMIM - HGNC]
  • SF3B3:splicing factor 3b subunit 3 [Gene - OMIM - HGNC]
  • SNTB2:syntrophin beta 2 [Gene - OMIM - HGNC]
  • TERB1:telomere repeat binding bouquet formation protein 1 [Gene - OMIM - HGNC]
  • TERF2:telomeric repeat binding factor 2 [Gene - OMIM - HGNC]
  • TXNL4B:thioredoxin like 4B [Gene - OMIM - HGNC]
  • TK2:thymidine kinase 2 [Gene - OMIM - HGNC]
  • TSNAXIP1:translin associated factor X interacting protein 1 [Gene - OMIM - HGNC]
  • TMED6:transmembrane p24 trafficking protein 6 [Gene - HGNC]
  • TMEM208:transmembrane protein 208 [Gene - OMIM - HGNC]
  • TANGO6:transport and golgi organization 6 homolog [Gene - OMIM - HGNC]
  • TPPP3:tubulin polymerization promoting protein family member 3 [Gene - OMIM - HGNC]
  • TAT:tyrosine aminotransferase [Gene - OMIM - HGNC]
  • LOC400541:uncharacterized LOC400541 [Gene]
  • VPS4A:vacuolar protein sorting 4 homolog A [Gene - OMIM - HGNC]
  • ZDHHC1:zinc finger DHHC-type containing 1 [Gene - HGNC]
  • ZNF19:zinc finger protein 19 [Gene - OMIM - HGNC]
  • ZNF23:zinc finger protein 23 [Gene - OMIM - HGNC]
  • ZNF821:zinc finger protein 821 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
16q21-22.2
Genomic location:
Chr16: 65821800 - 72146396 (on Assembly GRCh37)
Preferred name:
NC_000016.9:g.(?_65821800)_(72146396_?)del
HGVS:
NC_000016.9:g.(?_65821800)_(72146396_?)del

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003791084Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Mar 23, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003791084.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the ACD gene has been identified. The current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in ACD cause disease. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with ACD-related conditions.

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

Last Updated: Jun 9, 2024