NM_002448.3(MSX1):c.547C>T (p.Gln183Ter) AND MSX1-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 20, 2024
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV004542694.2

Allele description [Variation Report for NM_002448.3(MSX1):c.547C>T (p.Gln183Ter)]

NM_002448.3(MSX1):c.547C>T (p.Gln183Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

4p16.2

Genomic location:

Preferred name:

NM_002448.3(MSX1):c.547C>T (p.Gln183Ter)

HGVS:

NC_000004.12:g.4862778C>T
NG_008121.1:g.8114C>T
NG_101971.1:g.569C>T
NM_002448.3:c.547C>TMANE SELECT
NP_002439.2:p.Gln183Ter
LRG_1342t1:c.547C>T
LRG_1342:g.8114C>T
LRG_1342p1:p.Gln183Ter
NC_000004.11:g.4864505C>T

Protein change:

Q183*

Molecular consequence:

NM_002448.3:c.547C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: MSX1-related disorder
Synonyms:: MSX1-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004800406	PreventionGenetics, part of Exact Sciences	no assertion criteria provided	Likely pathogenic (Feb 20, 2024)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004800406

PreventionGenetics, part of Exact Sciences

no assertion criteria provided

Likely pathogenic
(Feb 20, 2024)

germline

clinical testing

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004800406.2

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

Description

The MSX1 c.547C>T variant is predicted to result in premature protein termination (p.Gln183*). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Nonsense variants in MSX1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

#	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 26, 2024

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