NM_000077.5(CDKN2A):c.174A>C (p.Arg58=) AND Melanoma-pancreatic cancer syndrome

Germline classification:: Benign (3 submissions)
Last evaluated:: Jul 7, 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:: RCV000411859.11

Allele description [Variation Report for NM_000077.5(CDKN2A):c.174A>C (p.Arg58=)]

NM_000077.5(CDKN2A):c.174A>C (p.Arg58=)

Gene:

CDKN2A:cyclin dependent kinase inhibitor 2A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p21.3

Genomic location:

Preferred name:

NM_000077.5(CDKN2A):c.174A>C (p.Arg58=)

Other names:

p.S73R:AGT>CGT; p.R58R:CGA>CGC

HGVS:

NC_000009.12:g.21971185T>G
NG_007485.1:g.28307A>C
NM_000077.5:c.174A>CMANE SELECT
NM_001195132.1:c.174A>C
NM_001195132.2:c.174A>C
NM_001363763.2:c.21A>C
NM_058195.4:c.217A>C
NM_058197.5:c.*97A>C
NP_000068.1:p.Arg58=
NP_000068.1:p.Arg58=
NP_001182061.1:p.Arg58=
NP_001350692.1:p.Arg7=
NP_478102.2:p.Ser73Arg
NP_478102.2:p.Ser73Arg
LRG_11t1:c.174A>C
LRG_11t2:c.217A>C
LRG_11:g.28307A>C
LRG_11p1:p.Arg58=
LRG_11p2:p.Ser73Arg
NC_000009.11:g.21971184T>G
NM_000077.3:c.174A>C
NM_000077.4:c.174A>C
NM_000077.5:c.174A>C
NM_058195.3:c.217A>C
NM_058197.4:c.*97A>C
p.=
p.R58R

Protein change:

S73R

Links:

dbSNP: rs201208890

NCBI 1000 Genomes Browser:

rs201208890

Molecular consequence:

NM_058197.5:c.*97A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_058195.4:c.217A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_000077.5:c.174A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001195132.2:c.174A>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001363763.2:c.21A>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000488970	Counsyl	criteria provided, single submitter (Counsyl Autosomal Dominant Disease Classification criteria (2015))	Benign (Jul 28, 2016)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9049826, 8561866, 16234564 Counsyl Autosomal Dominant Disease Classification criteria (2015), Citation Link,
SCV004017043	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004018561	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Apr 20, 2023)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000488970

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))

Benign
(Jul 28, 2016)

unknown

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Counsyl Autosomal Dominant Disease Classification criteria (2015),

Citation Link,

SCV004017043

KCCC/NGS Laboratory, Kuwait Cancer Control Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jul 7, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004018561

Myriad Genetics, Inc.

criteria provided, single submitter

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

Benign
(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	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

P16 deletion and mutation analysis in human brain tumors.

Barker FG, Chen P, Furman F, Aldape KD, Edwards MS, Israel MA.

J Neurooncol. 1997 Jan;31(1-2):17-23.

PubMed [citation]

PMID:: 9049826

Infrequent CDKN2 mutation in human differentiated thyroid cancers.

Tung WS, Shevlin DW, Bartsch D, Norton JA, Wells SA Jr, Goodfellow PJ.

Mol Carcinog. 1996 Jan;15(1):5-10.

PubMed [citation]

PMID:: 8561866

See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000488970.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	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 KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004017043.1

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

#	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

From Myriad Genetics, Inc., SCV004018561.1

#	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 considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.

#	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 8, 2024

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