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NM_001122630.2(CDKN1C):c.639_787+239del AND Beckwith-Wiedemann syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 12, 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:
RCV003613241.1

Allele description

NM_001122630.2(CDKN1C):c.639_787+239del

Gene:
CDKN1C:cyclin dependent kinase inhibitor 1C [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
11p15.4
Genomic location:
Preferred name:
NM_001122630.2(CDKN1C):c.639_787+239del
HGVS:
  • NC_000011.10:g.2884437_2884824del
  • NG_008022.1:g.5948_6335del
  • NG_121670.1:g.1_154del
  • NM_000076.2:c.672_820+239del
  • NM_001122630.2:c.639_787+239delMANE SELECT
  • NM_001122631.2:c.639_787+239del
  • NM_001362474.2:c.672_820+239del
  • NM_001362475.2:c.255+384_256-297del
  • LRG_533t1:c.672_820+239del
  • LRG_533:g.5948_6335del
  • NC_000011.9:g.2905661_2906048del
  • NC_000011.9:g.2905667_2906054del
Molecular consequence:
  • NM_001362475.2:c.255+384_256-297del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000076.2:c.672_820+239del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001122630.2:c.639_787+239del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001122631.2:c.639_787+239del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001362474.2:c.672_820+239del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Beckwith-Wiedemann syndrome (BWS)
Synonyms:
Exomphalos macroglossia gigantism syndrome; EMG Syndrome
Identifiers:
MONDO: MONDO:0007534; MedGen: C0004903; Orphanet: 116; OMIM: 130650

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004506332Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 12, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV004506332.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). This variant has not been reported in the literature in individuals affected with CDKN1C-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant results in the deletion of part of exon 1 (c.672_820+239del ) of the CDKN1C gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.

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

Last Updated: Feb 28, 2024