NM_000077.5(CDKN2A):c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] (p.Ala4_Pro11del) AND Melanoma-pancreatic cancer syndrome

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Apr 20, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000409781.5

Allele description [Variation Report for NM_000077.5(CDKN2A):c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] (p.Ala4_Pro11del)]

NM_000077.5(CDKN2A):c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] (p.Ala4_Pro11del)

Genes:

LOC130001603:ATAC-STARR-seq lymphoblastoid silent region 19811 [Gene]
CDKN2A:cyclin dependent kinase inhibitor 2A [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9p21.3

Genomic location:

Preferred name:

NM_000077.5(CDKN2A):c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] (p.Ala4_Pro11del)

HGVS:

NC_000009.11:g.21974795_21974818del
NC_000009.12:g.21974796GGCTCCATGCTGCTCCCCGCCGCC[1]
NG_007485.1:g.24649GGCGGCGGGGAGCAGCATGGAGCC[1]
NM_000077.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1]MANE SELECT
NM_000077.5:c.9_32del24
NM_001195132.2:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1]
NM_001363763.2:c.-3-3611_-3-3588del
NM_058195.4:c.194-3611_194-3588del
NM_058197.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1]
NP_000068.1:p.Ala4_Pro11del
NP_001182061.1:p.Ala4_Pro11del
NP_478104.2:p.Ala4_Pro11del
LRG_11t1:c.9_32del24
LRG_11:g.24649GGCGGCGGGGAGCAGCATGGAGCC[1]
NC_000009.11:g.21974795GGCTCCATGCTGCTCCCCGCCGCC[1]
NC_000009.11:g.21974795_21974818del
NC_000009.11:g.21974795_21974818delGGCTCCATGCTGCTCCCCGCCGCC
NM_000077.3:c.9_32del24
NM_000077.4:c.9_32del24
NM_000077.4:c.9_32delGGCGGCGGGGAGCAGCATGGAGCC
NM_000077.5:c.9_32delMANE SELECT
NM_000077.5:c.9_32del24MANE SELECT

Links:

dbSNP: rs587780668

NCBI 1000 Genomes Browser:

rs587780668

Molecular consequence:

NM_000077.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001195132.2:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_058197.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_000077.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001195132.2:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_058197.5:c.-16GGCGGCGGGGAGCAGCATGGAGCC[1] - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001363763.2:c.-3-3611_-3-3588del - intron variant - [Sequence Ontology: SO:0001627]
NM_058195.4:c.194-3611_194-3588del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Melanoma-pancreatic cancer syndrome
Identifiers:: MONDO: MONDO:0011713; MedGen: C1838547; Orphanet: 404560; OMIM: 606719

Recent activity

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PPP1R27 protein phosphatase 1 regulatory subunit 27 [Homo sapiens]
PPP1R27 protein phosphatase 1 regulatory subunit 27 [Homo sapiens]
Gene ID:116729

Gene
116729[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000489283	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Uncertain significance (Sep 13, 2016)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 25780468, 25803691, 10070944, 11159196, 17047042 Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV001137782	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Uncertain significance (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV004018547	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Uncertain significance (Apr 20, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000489283

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Uncertain significance
(Sep 13, 2016)

unknown

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV001137782

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Uncertain significance
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV004018547

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))

Uncertain significance
(Apr 20, 2023)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Prevalence and predictors of germline CDKN2A mutations for melanoma cases from Australia, Spain and the United Kingdom.

Harland M, Cust AE, Badenas C, Chang YM, Holland EA, Aguilera P, Aitken JF, Armstrong BK, Barrett JH, Carrera C, Chan M, Gascoyne J, Giles GG, Agha-Hamilton C, Hopper JL, Jenkins MA, Kanetsky PA, Kefford RF, Kolm I, Lowery J, Malvehy J, Ogbah Z, et al.

Hered Cancer Clin Pract. 2014;12(1):20. doi: 10.1186/1897-4287-12-20.

PubMed [citation]

PMID:: 25780468
PMCID:: PMC4361137

Molecular characterization of melanoma cases in Denmark suspected of genetic predisposition.

Wadt KA, Aoude LG, Krogh L, Sunde L, Bojesen A, Grønskov K, Wartacz N, Ek J, Tolstrup-Andersen M, Klarskov-Andersen M, Borg Å, Heegaard S, Kiilgaard JF, Hansen TV, Klein K, Jönsson G, Drzewiecki KT, Dunø M, Hayward NK, Gerdes AM.

PLoS One. 2015;10(3):e0122662. doi: 10.1371/journal.pone.0122662.

PubMed [citation]

PMID:: 25803691
PMCID:: PMC4372390

See all PubMed Citations (5)

Details of each submission

From Counsyl, SCV000489283.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

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

From Mendelics, SCV001137782.2

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

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

From Myriad Genetics, Inc., SCV004018547.2

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

Description

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

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

Last Updated: Oct 26, 2024

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