NM_004064.5(CDKN1B):c.-31AG[1] AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jun 13, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000994850.33

Allele description [Variation Report for NM_004064.5(CDKN1B):c.-31AG[1]]

NM_004064.5(CDKN1B):c.-31AG[1]

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

12p13.1

Genomic location:

Preferred name:

NM_004064.5(CDKN1B):c.-31AG[1]

HGVS:

NC_000012.11:g.12870742_12870745delGAGA
NC_000012.12:g.12717809AG[1]
NG_016341.1:g.5442AG[1]
NM_004064.5:c.-31AG[1]MANE SELECT
NC_000012.11:g.12870742_12870745del
NC_000012.11:g.12870742_12870745delGAGA
NC_000012.11:g.12870743AG[1]
NC_000012.12:g.12717808_12717811delGAGA
NM_004064.3:c.-29_-26delAGAG
NM_004064.4:c.-29_-26delAGAG
NM_004064.5:c.-29_-26delAGAGMANE SELECT

Links:

OMIM: 600778.0004; dbSNP: rs774454456

NCBI 1000 Genomes Browser:

rs774454456

Molecular consequence:

NM_004064.5:c.-31AG[1] - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001148641	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Sep 1, 2023)	germline	clinical testing	Citation Link,
SCV002319178	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jun 13, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001148641

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Sep 1, 2023)

germline

clinical testing

Citation Link,

SCV002319178

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jun 13, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	10	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV001148641.26

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	10	not provided	not provided	clinical testing	not provided

Description

CDKN1B: PS3:Moderate, BP4, BS1

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		10	not provided	not provided	not provided

From GeneDx, SCV002319178.6

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

Description

Published functional studies demonstrate a damaging effect: decreased transcriptional activity, reduced p27 mRNA, and increased cytoplasmic localization (PMID: 22129891, 25645465, 27038812); Identified in patients with clinical features of Multiple Endocrine Neoplasia syndrome type 4 (MEN4) in published literature, but inherited from an unaffected parent in at least one family (PMID: 22129891, 25645465, 27038812, 32232325); Deleted nucleotides are not conserved across species; Also known as c.-32_-29del; This variant is associated with the following publications: (PMID: 27038812, 28824003, 25645465, 26054904, 27657986, 24819502, 30555957, 32232325, 34426522, 30065701, 35355569, 30990521, 36520683, 22129891)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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