NM_002386.4(MC1R):c.887_888del (p.Leu296fs) AND Melanoma, cutaneous malignant, susceptibility to, 5

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 2023
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:: RCV003629015.2

Allele description [Variation Report for NM_002386.4(MC1R):c.887_888del (p.Leu296fs)]

NM_002386.4(MC1R):c.887_888del (p.Leu296fs)

Gene:

MC1R:melanocortin 1 receptor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_002386.4(MC1R):c.887_888del (p.Leu296fs)

HGVS:

NC_000016.10:g.89920145_89920146del
NG_012026.1:g.7267_7268del
NG_027810.1:g.3137_3138del
NG_134986.2:g.1729_1730del
NM_002386.4:c.887_888delMANE SELECT
NP_002377.4:p.Leu296fs
NC_000016.9:g.89986552_89986553del
NC_000016.9:g.89986553_89986554del

Protein change:

L296fs

Molecular consequence:

NM_002386.4:c.887_888del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Melanoma, cutaneous malignant, susceptibility to, 5
Synonyms:: Cutaneous malignant melanoma 5
Identifiers:: MONDO: MONDO:0013133; MedGen: C2751295; Orphanet: 618; OMIM: 613099

Recent activity

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small nuclear ribonucleoprotein [Thermoplasma volcanium GSS1]
small nuclear ribonucleoprotein [Thermoplasma volcanium GSS1]
gi|13541187|ref|NP_110875.1|

Protein
Anaeromassilibacillus sp. An250 isolate Chicken_18_mag_111 genome assembly, cont...
Anaeromassilibacillus sp. An250 isolate Chicken_18_mag_111 genome assembly, contig: MAGpy_11413_18_idba_bin_111_fascaffold_169, whole genome shotgun sequence
gi|1908931965|emb|CAJFIB010000004.1

Nucleotide
Uncultured Eggerthellaceae bacterium isolate Coassembly_mag_450, whole genome sh...
Uncultured Eggerthellaceae bacterium isolate Coassembly_mag_450, whole genome shotgun sequencing project
gi|1908968786|emb|CAJFUR000000000.1 UR010000000

Nucleotide
zinc finger protein 219 [Homo sapiens]
zinc finger protein 219 [Homo sapiens]
gi|156416026|ref|NP_001095924.1|

Protein
Taxonomy Links for Protein (Select 18043293) (1)
Taxonomy

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004516091	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2023)	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

SCV004516091

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2023)

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, SCV004516091.1

#	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 creates a premature translational stop signal (p.Leu296Hisfs*38) in the MC1R gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 22 amino acid(s) of the MC1R protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MC1R-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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