NM_001122630.2(CDKN1C):c.85G>T (p.Glu29Ter) AND Beckwith-Wiedemann syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 17, 2019
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:: RCV001219770.5

Allele description [Variation Report for NM_001122630.2(CDKN1C):c.85G>T (p.Glu29Ter)]

NM_001122630.2(CDKN1C):c.85G>T (p.Glu29Ter)

Gene:

CDKN1C:cyclin dependent kinase inhibitor 1C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_001122630.2(CDKN1C):c.85G>T (p.Glu29Ter)

HGVS:

NC_000011.10:g.2885372C>A
NG_008022.1:g.5394G>T
NM_000076.2:c.118G>T
NM_001122630.2:c.85G>TMANE SELECT
NM_001122631.2:c.85G>T
NM_001362474.2:c.118G>T
NM_001362475.2:c.85G>T
NP_000067.1:p.Glu40Ter
NP_001116102.1:p.Glu29Ter
NP_001116103.1:p.Glu29Ter
NP_001349403.1:p.Glu40Ter
NP_001349404.1:p.Glu29Ter
LRG_533t1:c.118G>T
LRG_533:g.5394G>T
LRG_533p1:p.Glu40Ter
NC_000011.9:g.2906602C>A

Protein change:

E29*

Links:

dbSNP: rs1564930723

NCBI 1000 Genomes Browser:

rs1564930723

Molecular consequence:

NM_000076.2:c.118G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001122630.2:c.85G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001122631.2:c.85G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362474.2:c.118G>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001362475.2:c.85G>T - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001391725	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 17, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 20503313, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001391725

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 17, 2019)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

CDKN1C (p57(Kip2)) analysis in Beckwith-Wiedemann syndrome (BWS) patients: Genotype-phenotype correlations, novel mutations, and polymorphisms.

Romanelli V, Belinchón A, Benito-Sanz S, Martínez-Glez V, Gracia-Bouthelier R, Heath KE, Campos-Barros A, García-Miñaur S, Fernandez L, Meneses H, López-Siguero JP, Guillén-Navarro E, Gómez-Puertas P, Wesselink JJ, Mercado G, Esteban-Marfil V, Palomo R, Mena R, Sánchez A, Del Campo M, Lapunzina P.

Am J Med Genet A. 2010 Jun;152A(6):1390-7. doi: 10.1002/ajmg.a.33453. Review.

PubMed [citation]

PMID:: 20503313

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001391725.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Glu40*) in the CDKN1C gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CDKN1C-related conditions. Loss-of-function variants in CDKN1C are known to be pathogenic (PMID: 20503313). For these reasons, this variant has been classified as Pathogenic.

#	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 20, 2024

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