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NM_002449.5(MSX2):c.116G>T (p.Arg39Leu) AND Cranium bifidum occultum

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 6, 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:
RCV002914244.3

Allele description [Variation Report for NM_002449.5(MSX2):c.116G>T (p.Arg39Leu)]

NM_002449.5(MSX2):c.116G>T (p.Arg39Leu)

Gene:
MSX2:msh homeobox 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q35.2
Genomic location:
Preferred name:
NM_002449.5(MSX2):c.116G>T (p.Arg39Leu)
HGVS:
  • NC_000005.10:g.174724775G>T
  • NG_008124.1:g.5204G>T
  • NM_001363626.2:c.116G>T
  • NM_002449.5:c.116G>TMANE SELECT
  • NP_001350555.1:p.Arg39Leu
  • NP_002440.2:p.Arg39Leu
  • NC_000005.9:g.174151778G>T
  • NM_002449.4:c.116G>T
Protein change:
R39L
Molecular consequence:
  • NM_001363626.2:c.116G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002449.5:c.116G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cranium bifidum occultum
Synonyms:
CRANIUM BIFIDUM, HEREDITARY; Enlarged parietal foramina; CATLIN MARKS
Identifiers:
MedGen: C1868598; Human Phenotype Ontology: HP:0004423

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003259298Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 6, 2023) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV003259298.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt MSX2 protein function. ClinVar contains an entry for this variant (Variation ID: 2049884). This variant has not been reported in the literature in individuals affected with MSX2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 39 of the MSX2 protein (p.Arg39Leu).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024