NM_004064.5(CDKN1B):c.1_15del (p.Met1_Arg5del) AND Multiple endocrine neoplasia type 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 13, 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:: RCV001233560.6

Allele description [Variation Report for NM_004064.5(CDKN1B):c.1_15del (p.Met1_Arg5del)]

NM_004064.5(CDKN1B):c.1_15del (p.Met1_Arg5del)

Gene:

CDKN1B:cyclin dependent kinase inhibitor 1B [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12p13.1

Genomic location:

Preferred name:

NM_004064.5(CDKN1B):c.1_15del (p.Met1_Arg5del)

HGVS:

NC_000012.12:g.12717840_12717854del
NG_016341.1:g.5473_5487del
NM_004064.5:c.1_15delMANE SELECT
NP_004055.1:p.Met1_Arg5del
NC_000012.11:g.12870774_12870788del
NM_004064.3:c.1_15del15
NM_004064.4:c.1_15del

Links:

dbSNP: rs758613901

NCBI 1000 Genomes Browser:

rs758613901

Molecular consequence:

NM_004064.5:c.1_15del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_004064.5:c.1_15del - initiator_codon_variant - [Sequence Ontology: SO:0001582]

Condition(s)

Name:: Multiple endocrine neoplasia type 4
Synonyms:: MULTIPLE ENDOCRINE NEOPLASIA, TYPE IV
Identifiers:: MONDO: MONDO:0012552; MedGen: C1970712; OMIM: 610755

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001406162	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 13, 2022)	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

SCV001406162

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 13, 2022)

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, SCV001406162.6

#	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 affects the initiator methionine of the CDKN1B mRNA. The next in-frame methionine is located at codon 16. This variant is present in population databases (rs758613901, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with CDKN1B-related conditions. ClinVar contains an entry for this variant (Variation ID: 960097). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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: Sep 29, 2024

ClinVar

Relating variation to medicine