NM_030662.4(MAP2K2):c.1140C>T (p.Ala380=) AND RASopathy

Germline classification:: Likely benign (2 submissions)
Last evaluated:: May 9, 2017
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000521790.10

Allele description [Variation Report for NM_030662.4(MAP2K2):c.1140C>T (p.Ala380=)]

NM_030662.4(MAP2K2):c.1140C>T (p.Ala380=)

Gene:

MAP2K2:mitogen-activated protein kinase kinase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_030662.4(MAP2K2):c.1140C>T (p.Ala380=)

Other names:

p.A380A:GCC>GCT; NM_030662.3(MAP2K2):c.1140C>T

HGVS:

NC_000019.10:g.4090661G>A
NG_007996.1:g.38468C>T
NM_030662.4:c.1140C>TMANE SELECT
NP_109587.1:p.Ala380=
NP_109587.1:p.Ala380=
LRG_750t1:c.1140C>T
LRG_750:g.38468C>T
LRG_750p1:p.Ala380=
NC_000019.9:g.4090659G>A
NM_030662.3:c.1140C>T
c.1140C>T
p.Ala380Ala

Links:

dbSNP: rs146618055

NCBI 1000 Genomes Browser:

rs146618055

Molecular consequence:

NM_030662.4:c.1140C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: RASopathy
Synonyms:: rasopathies; Noonan spectrum disorder
Identifiers:: MONDO: MONDO:0021060; MedGen: C5555857

Recent activity

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Chromosome neighbors for GEO Profiles (Select 131322500) (18)
GEO Profiles
Escherichia coli
Escherichia coli
CVM NARMS Escherichia coli

BioProject
BioProject Links for Nucleotide (Select 1516357710) (1)
BioProject
DLSTP1 dihydrolipoamide S-succinyltransferase pseudogene 1 [Homo sapiens]
DLSTP1 dihydrolipoamide S-succinyltransferase pseudogene 1 [Homo sapiens]
Gene ID:1744

Gene
Gene Links for GEO Profiles (Select 131322500) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000616562	ClinGen RASopathy Variant Curation Expert Panel	reviewed by expert panel (ClinGen RASopathy ACMG Specifications v1)	Likely benign (May 9, 2017)	germline	curation	Citation Link,
SCV001000776	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 29, 2024)	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

SCV000616562

ClinGen RASopathy Variant Curation Expert Panel

reviewed by expert panel

(ClinGen RASopathy ACMG Specifications v1)

Likely benign
(May 9, 2017)

germline

curation

Citation Link,

SCV001000776

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 29, 2024)

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, curation

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 ClinGen RASopathy Variant Curation Expert Panel, SCV000616562.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	not provided

Description

The filtering allele frequency of the c.1140C>T (p.Ala380=) variant in the MAP2K2 gene is 0.003% (2/796) of East Asian chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as likely benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BS1; PMID:29493581)

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001000776.6

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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