VCV002108584.3 - ClinVar

NM_005378.6(MYCN):c.621dup (p.Ala208fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic/Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_005378.6(MYCN):c.621dup (p.Ala208fs)

Variation ID: 2108584 Accession: VCV002108584.3

Type and length

Duplication, 1 bp

Location

Cytogenetic: 2p24.3 2: 15942684-15942685 (GRCh38) [ NCBI UCSC ] 2: 16082806-16082807 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Feb 20, 2024	Aug 8, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_005378.6:c.621dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_005369.2:p.Ala208fs	frameshift
NM_001293228.2:c.621dup	NP_001280157.1:p.Ala208fs	frameshift
NM_001293231.2:c.157+1942dup		intron variant
NM_001293233.2:c.*556dup		3 prime UTR
NC_000002.12:g.15942685dup
NC_000002.11:g.16082807dup
NG_007457.1:g.7125dup
NG_007457.2:g.7137dup

... more HGVS ... less HGVS

Protein change

A208fs

Other names

Canonical SPDI

NC_000002.12:15942684:A:AA

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MYCN		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	166	266

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
not provided	Pathogenic (1)	criteria provided, single submitter	Sep 14, 2022	RCV003017687.3
Feingold syndrome type 1	Likely pathogenic (1)	criteria provided, single submitter	Aug 8, 2023	RCV003455662.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Aug 08, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Feingold syndrome type 1 Affected status: yes Allele origin: germline	Clinical Genomics Laboratory, Washington University in St. Louis Accession: SCV004177161.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023	Comment: The MYCN c.621dup (p.Ala208fs) variant, to our knowledge, has not been reported in the medical literature but has been reported in the ClinVar database as … (more) The MYCN c.621dup (p.Ala208fs) variant, to our knowledge, has not been reported in the medical literature but has been reported in the ClinVar database as a germline pathogenic variant by a single submitter. This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant causes a frameshift by duplicating a single nucleotide, leading to a premature termination codon; however, because this occurs in the penultimate exon more than 100 nucleotides from the last exon junction complex, it is uncertain if this would lead to nonsense mediated decay. Additionally, other variants that introduce a nonsense codon in this region and downstream have been reported in affected individuals and are considered pathogenic (Blaumeiser B et al., PMID: 18671284; Cognet M et al., PMID: 21224895). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic. (less)
Pathogenic (Sep 14, 2022)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003325558.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 20, 2024	Publications: PubMed (1) PubMed: 15821734 Comment: This sequence change creates a premature translational stop signal (p.Ala208Serfs58) in the MYCN gene. While this is not anticipated to result in nonsense mediated decay, … (more) This sequence change creates a premature translational stop signal (p.Ala208Serfs58) in the MYCN gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 257 amino acid(s) of the MYCN protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the MYCN protein in which other variant(s) (p.Arg373*) have been determined to be pathogenic (PMID: 15821734). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with MYCN-related conditions. This variant is not present in population databases (gnomAD no frequency). (less)

Comment:

The MYCN c.621dup (p.Ala208fs) variant, to our knowledge, has not been reported in the medical literature but has been reported in the ClinVar database as a germline pathogenic variant by a single submitter. This variant is absent from the general population (gnomAD v.2.1.1), indicating it is not a common variant. This variant causes a frameshift by duplicating a single nucleotide, leading to a premature termination codon; however, because this occurs in the penultimate exon more than 100 nucleotides from the last exon junction complex, it is uncertain if this would lead to nonsense mediated decay. Additionally, other variants that introduce a nonsense codon in this region and downstream have been reported in affected individuals and are considered pathogenic (Blaumeiser B et al., PMID: 18671284; Cognet M et al., PMID: 21224895). Based on available information and the ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as likely pathogenic.

Comment:

This sequence change creates a premature translational stop signal (p.Ala208Serfs*58) in the MYCN gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 257 amino acid(s) of the MYCN protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the MYCN protein in which other variant(s) (p.Arg373*) have been determined to be pathogenic (PMID: 15821734). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with MYCN-related conditions. This variant is not present in population databases (gnomAD no frequency).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
MYCN haploinsufficiency is associated with reduced brain size and intestinal atresias in Feingold syndrome.	van Bokhoven H	Nature genetics	2005	PMID: 15821734

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_005378.6(MYCN):c.621dup (p.Ala208fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...