NM_000075.4(CDK4):c.889_903del (p.Lys297_Asn301del) AND Familial melanoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 9, 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:: RCV003059731.3

Allele description [Variation Report for NM_000075.4(CDK4):c.889_903del (p.Lys297_Asn301del)]

NM_000075.4(CDK4):c.889_903del (p.Lys297_Asn301del)

Genes:

CDK4:cyclin dependent kinase 4 [Gene - OMIM - HGNC]
TSPAN31:tetraspanin 31 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

12q14.1

Genomic location:

Preferred name:

NM_000075.4(CDK4):c.889_903del (p.Lys297_Asn301del)

HGVS:

NC_000012.12:g.57748536_57748550del
NG_007484.2:g.8834_8848del
NM_000075.4:c.889_903delMANE SELECT
NM_001330168.2:c.*1246_*1260del
NM_001330169.2:c.*1246_*1260del
NM_005981.5:c.*1246_*1260delMANE SELECT
NP_000066.1:p.Lys297_Asn301del
NP_000066.1:p.Lys297_Asn301del
LRG_490t1:c.887_901del
LRG_490:g.8834_8848del
LRG_490p1:p.Lys297_Asn301del
NC_000012.11:g.58142317_58142331del
NC_000012.11:g.58142319_58142333del
NM_000075.2:c.887_901delATAAGGATGAAGGTA

Molecular consequence:

NM_001330168.2:c.*1246_*1260del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001330169.2:c.*1246_*1260del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_005981.5:c.*1246_*1260del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_000075.4:c.889_903del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Familial melanoma
Synonyms:: Hereditary melanoma; Hereditary cutaneous melanoma
Identifiers:: MONDO: MONDO:0018961; MedGen: C1512419

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003354364	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 9, 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

SCV003354364

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 9, 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, SCV003354364.2

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

Description

This variant, c.889_903del, results in the deletion of 5 amino acid(s) of the CDK4 protein (p.Lys297_Asn301del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDK4-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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

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