NM_001122630.2(CDKN1C):c.775C>A (p.Pro259Thr) AND Beckwith-Wiedemann syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 23, 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:: RCV000524779.5

Allele description [Variation Report for NM_001122630.2(CDKN1C):c.775C>A (p.Pro259Thr)]

NM_001122630.2(CDKN1C):c.775C>A (p.Pro259Thr)

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.775C>A (p.Pro259Thr)

HGVS:

NC_000011.10:g.2884682G>T
NG_008022.1:g.6084C>A
NM_000076.2:c.808C>A
NM_001122630.2:c.775C>AMANE SELECT
NM_001122631.2:c.775C>A
NM_001362474.2:c.808C>A
NM_001362475.2:c.255+520C>A
NP_000067.1:p.Pro270Thr
NP_001116102.1:p.Pro259Thr
NP_001116103.1:p.Pro259Thr
NP_001349403.1:p.Pro270Thr
LRG_533t1:c.808C>A
LRG_533:g.6084C>A
LRG_533p1:p.Pro270Thr
NC_000011.9:g.2905912G>T

Protein change:

P259T

Links:

dbSNP: rs1416211722

NCBI 1000 Genomes Browser:

rs1416211722

Molecular consequence:

NM_001362475.2:c.255+520C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_000076.2:c.808C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001122630.2:c.775C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001122631.2:c.775C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001362474.2:c.808C>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000623182	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 23, 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

SCV000623182

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 23, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000623182.5

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

Description

This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 270 of the CDKN1C protein (p.Pro270Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDKN1C-related conditions. ClinVar contains an entry for this variant (Variation ID: 454033). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CDKN1C protein function. 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.

#	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 28, 2024

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