VCV002672096.2 - ClinVar

NM_002755.4(MAP2K1):c.306_311del (p.Ile103_Lys104del)

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_002755.4(MAP2K1):c.306_311del (p.Ile103_Lys104del)

Variation ID: 2672096 Accession: VCV002672096.2

Type and length

Deletion, 6 bp

Location

Cytogenetic: 15q22.31 15: 66436759-66436764 (GRCh38) [ NCBI UCSC ] 15: 66729097-66729102 (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	Dec 25, 2023	Sep 29, 2024	Oct 18, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_002755.4:c.306_311del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002746.1:p.Ile103_Lys104del	inframe deletion
NM_001411065.1:c.240_245del	NP_001397994.1:p.Ile81_Lys82del	inframe deletion
NM_002755.3:c.306_311del
NC_000015.10:g.66436760_66436765del
NC_000015.9:g.66729098_66729103del
NG_008305.1:g.54888_54893del
LRG_725:g.54888_54893del
LRG_725t1:c.306_311del	LRG_725p1:p.Ile103_Lys104del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000015.10:66436758:AGATCAA:A

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.
MAP2K1		No evidence available	No evidence available	GRCh38 GRCh37	515	606

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.
Vascular malformation	Likely pathogenic (1)	criteria provided, single submitter	Oct 18, 2023	RCV003458964.1
not provided	Pathogenic (1)	criteria provided, single submitter	-	RCV004719331.1

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 (Oct 18, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Vascular malformation Affected status: yes Allele origin: somatic	Clinical Genomics Laboratory, Washington University in St. Louis Accession: SCV004176938.1 First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023	Comment: The MAP2K1 c.306_311del (p.Ile103_Lys104del) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in individuals with spitzoid melanocytic … (more) The MAP2K1 c.306_311del (p.Ile103_Lys104del) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in individuals with spitzoid melanocytic lesions (Kerckhoffs KGP et al., PMID: 33040161; Zaremba A et al., PMID: 35737508); however, have not been reported in association with vascular malformations. This variant has been reported in multiple cancer cases as a somatic variant in the cancer database COSMIC (COSMIC ID: COSV61069477). This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. Functional studies show that this variant leads to RAS-independent autophosphorylation and activation of downstream pERK and pMEK pathways, indicating that this variant impacts protein function (Gao Y et al., PMID: 29483135; Mizuno S et al., PMID: 36442478). This variant is predicted to cause a change in the length of the protein due to an in-frame deletion of 2 amino acids in a non-repeat region. Based on an internally developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868) and gene-specific practices from the ClinGen Criteria Specification Registry, the MAP2K1 c.306_311del (p.Ile103_Lys104del) variant is classified as likely pathogenic. (less)
Pathogenic (-)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	not provided Affected status: yes Allele origin: somatic	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital Accession: SCV005326302.1 First in ClinVar: Sep 29, 2024 Last updated: Sep 29, 2024	Comment: The p.Ile103_Lys104del variant results in loss of 6 nucleotides leading to an activating in-frame deletion within the MAP2K1 catalytic kinase domain. This variant has not … (more) The p.Ile103_Lys104del variant results in loss of 6 nucleotides leading to an activating in-frame deletion within the MAP2K1 catalytic kinase domain. This variant has not been observed in large population studies (gnomAD v2.1.1). This variant has previously been reported in several individuals with spitz nevus, a melanocytic proliferation caused by MAPK pathway hyperactivation (PMID: 33040161, PMID: 35457030, PMID: 22082838). (less) Clinical Features: Arteriovenous malformation (present)

Comment:

The MAP2K1 c.306_311del (p.Ile103_Lys104del) variant was identified at an allelic fraction consistent with somatic origin. This variant has been reported in individuals with spitzoid melanocytic lesions (Kerckhoffs KGP et al., PMID: 33040161; Zaremba A et al., PMID: 35737508); however, have not been reported in association with vascular malformations. This variant has been reported in multiple cancer cases as a somatic variant in the cancer database COSMIC (COSMIC ID: COSV61069477). This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. Functional studies show that this variant leads to RAS-independent autophosphorylation and activation of downstream pERK and pMEK pathways, indicating that this variant impacts protein function (Gao Y et al., PMID: 29483135; Mizuno S et al., PMID: 36442478). This variant is predicted to cause a change in the length of the protein due to an in-frame deletion of 2 amino acids in a non-repeat region. Based on an internally developed protocol informed by the ACMG/AMP guidelines (Richards S et al., PMID: 25741868) and gene-specific practices from the ClinGen Criteria Specification Registry, the MAP2K1 c.306_311del (p.Ile103_Lys104del) variant is classified as likely pathogenic.

Comment:

The p.Ile103_Lys104del variant results in loss of 6 nucleotides leading to an activating in-frame deletion within the MAP2K1 catalytic kinase domain. This variant has not been observed in large population studies (gnomAD v2.1.1). This variant has previously been reported in several individuals with spitz nevus, a melanocytic proliferation caused by MAPK pathway hyperactivation (PMID: 33040161, PMID: 35457030, PMID: 22082838).

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

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Oct 08, 2024

ClinVar Genomic variation as it relates to human health

NM_002755.4(MAP2K1):c.306_311del (p.Ile103_Lys104del)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...