NM_002448.3(MSX1):c.682_683del (p.Lys228fs) AND Hypoplastic enamel-onycholysis-hypohidrosis syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 26, 2019
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:: RCV001036941.8

Allele description [Variation Report for NM_002448.3(MSX1):c.682_683del (p.Lys228fs)]

NM_002448.3(MSX1):c.682_683del (p.Lys228fs)

Gene:

MSX1:msh homeobox 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4p16.2

Genomic location:

Preferred name:

NM_002448.3(MSX1):c.682_683del (p.Lys228fs)

HGVS:

NC_000004.12:g.4862913_4862914del
NG_008121.1:g.8249_8250del
NM_002448.3:c.682_683delMANE SELECT
NP_002439.2:p.Lys228fs
LRG_1342t1:c.682_683del
LRG_1342:g.8249_8250del
LRG_1342p1:p.Lys228fs
NC_000004.11:g.4864639_4864640del
NC_000004.11:g.4864640_4864641del

Protein change:

K228fs

Links:

dbSNP: rs1737950636

NCBI 1000 Genomes Browser:

rs1737950636

Molecular consequence:

NM_002448.3:c.682_683del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hypoplastic enamel-onycholysis-hypohidrosis syndrome (TNS)
Synonyms:: NAIL DYSPLASIA WITH HYPODONTIA; Witkop syndrome; Dysplasia of nails with hypodontia; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008582; MedGen: C0406735; Orphanet: 2228; OMIM: 189500

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001200331	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 26, 2019)	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

SCV001200331

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 26, 2019)

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, SCV001200331.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the affected amino acid(s) is currently unknown. This variant has not been reported in the literature in individuals with MSX1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change results in a premature translational stop signal in the MSX1 gene (p.Lys228Glufs*111). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 76 amino acids of the MSX1 protein.

#	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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